Whale Sharks are found in both coastal and oceanic habitats (Rowat and Brooks 2012). Oceanic sightings are strongly correlated with temperature in the Indian and Atlantic oceans (Sequeira et al. 2014), with most occurring between 26.5° and 30°C in the Indian Ocean (Sequeira et al. 2012). Depth was an important predictor in the Atlantic and Pacific Oceans, but was not significant in the Indian Ocean (Sequeira et al. 2014). Whale Sharks are highly mobile, with mean daily movement rates of 24–28 km based on tethered geopositioning tags (Hueter et al. 2013). Cyclical or longer-term climate shifts affect Whale Shark occurrence and abundance (Sleeman et al. 2010, Sequeira et al. 2012), which needs to be considered when discussing local abundance trends.

Whale Sharks spend the majority of time in the epipelagic zone, but dive to at least 1,928 m in depth (Tyminsky et al. 2015). The driver of these deep dives is unclear, but may be related to foraging behaviour, especially when crossing oceanic waters with comparatively low surface productivity (Sleeman et al. 2010, Brunnschweiler and Sims 2011, Tyminsky et al. 2015) and/or assist with energy conservation when moving between prey zones (Gleiss et al. 2011) or navigating (Tyminsky et al. 2015). Initial results from fatty acid dietary studies suggest that meso- and bathypelagic prey may be an important component of Whale Shark diet (Rohner et al. 2013), and dive data from pop-up archival tags provide some evidence for mesopelagic foraging behaviour (Tyminsky et al. 2015).

Most Whale Shark sightings occur at a small number of known coastal feeding areas for the species, where the sharks aggregate on the surface to exploit seasonal productivity such as fish spawning events or zooplankton blooms (Rowat and Brooks 2012). A degree of inter-annual site fidelity has been documented in many locations (Cagua et al. 2015, Norman et al. submitted). Sexual- and size-based segregation is typical in these locations, with a bias towards juvenile males from 4–8 m length (Rohner et al. 2015, Norman et al. submitted). This pronounced segregation indicates that ontogenetic and sex-specific habitat or dietary shifts are present in the species. In the Gulf of California, juvenile sharks, comprising 60% males, were found in shallower waters exploiting abundant prey. Larger sharks, composed of 84% females, occurred in oceanic waters where they fed on diffuse patches of euphasiids (Ketchum et al. 2012). An initial stable isotope study of Indian Whale Sharks showed a positive relationship between size and δ¹³C and δ¹⁵N, suggesting that larger sharks feed on prey items of a larger size and higher trophic level (Borrell et al. 2011). Females had lower values of δ¹³C and δ¹⁵N than males (Borrell et al. 2011) suggesting that they have a different, more pelagic diet, while individuals of <4 m total length (TL) also showed a lower δ13C than larger individuals suggesting a transition from pelagic to more coastal foraging habitats.

The largest recorded Whale Shark, approximately 20 m TL (Chen et al. 1997) and 42 t in mass (Hsu et al. 2014), have been reported from Taiwan. An individual extrapolated to be 18.8 m TL was caught in India (Borrell et al. 2011). Norman and Stevens (2007) found that 50% of males were mature, based on clasper morphology, at a visually estimated TL of 8.1 m in Western Australia, while 50% maturity was estimated to occur at 9.2 m TL using laser photogrammetry in Mozambique (Rohner et al. 2015). In the Gulf of Mexico, Ramírez-Macías et al. (2012) visually estimated 50% male maturity to occur at around 7 m TL. Given the genetic differentiation between the Indo-Pacific and Atlantic Oceans (Vignaud et al. 2014), this may represent a subpopulation-level difference in the size of maturation. Size at maturity in female sharks is approximately 9 m TL, based on visual (Acuña-Marrero et al. 2014, Ramírez-Macías et al. 2012) and laser photogrammetric estimates (Acuña-Marrero et al. 2014) from the Eastern Pacific, and a 9.6 m TL individual recorded from Taiwan (Hsu et al. 2014). All of seven stranded female specimens from 4.8 to 8.7 m TL in South Africa were immature (Beckley et al. 1997). The only confirmed pregnant female examined, from Taiwan, was 10.6 m TL (Joung et al. 1996).

Whale Shark reproductive ecology is poorly known. Pregnant female sharks are seasonally found in the Eastern Pacific, particularly off Darwin Island in the Galapagos Archipelago (Acuña-Marrero et al. 2014) and the Gulf of California (Eckert and Stewart 2001, Ramírez-Macías et al. 2012), but rarely sighted outside this region. An exception is St Helena Island in the mid-Atlantic, where pregnant female sharks are routinely observed on a seasonal basis (A. Dove, pers. comm). The single pregnant female that has been physically examined, from Taiwan, had 304 pups in various stages of development, the largest litter size reported from any shark species (Joung et al. 1996, Schmidt et al. 2010). This discovery established that Whale Sharks are aplacental viviparous. Paternity analysis on a subset of the offspring established that a single male might have sired the entire litter, suggesting that the species has the capacity to store sperm (Schmidt et al. 2010). The largest size class of embryos, 58–64 cm TL, appeared close to fully developed (Joung et al. 1996). The smallest free-swimming neonate found in the wild, from the Philippines, was 46 cm TL (Aca and Schmidt 2011). Size at birth is therefore presumed to be around this range (Aca and Schmidt 2011). Reproductive periodicity is unknown: resightings rarely occur in the areas where pregnant sharks are observed (Norman et al. submitted).

Age and growth data on Whale Shark are sparse. Stranded sharks in South Africa (Wintner 2000) and fishery catches in Taiwan (Hsu et al. 2014), respectively, have been assessed. Both studies were limited by small sample sizes of predominantly juvenile sharks. Hsu et al. (2014) concluded that growth band deposition is likely to be biannual and, based on this, estimated that male sharks begin maturing at ~17 years and females at 19–22 years in the Indo-Pacific. However, these estimates have some important caveats: biannual band deposition has been demonstrated in very few other shark species, and other orectolobiform species have been shown to have aperiodic band pair formation (Huveneers et al. 2013). Validation through wild growth studies is important to confirm these results. Initial results from laser photogrammetric studies indicate that growth increments over periods of 1–3 years are too small to be accurately measured, but the technique may have value over longer time-frames (Rohner et al. 2015). Generation length is estimated as 25 years.

Major contemporary threats to Whale Sharks include fisheries catches, bycatch in nets, and vessel strikes. Other threats affect Whale Shark on local or regional scales.  

Whale Sharks are presently fished in several locations. In southern China, large-scale commercial take of Whale Sharks appears to be increasing (Li et al. 2012). Although Whale Sharks are not necessarily targeted, they are routinely captured and retained when sighted (Li et al. 2012). A small-scale opportunistic fishery for Whale Sharks is also present in Oman (D. Robinson, pers. comm). 

Whale Sharks have previously been targeted in large-scale fisheries from India, the Philippines and Taiwan, with hundreds of sharks caught annually in each country until species-level protections were implemented (Rowat and Brooks 2012). A smaller directed fishery occurred in the Maldives until Whale Sharks were protected in 1995 (Anderson and Ahmed 1993). Broader-scale subpopulation reduction caused by these fisheries was raised as a possible driver of declining sightings in Thailand (Theberge and Dearden 2006) and Western Australia (Bradshaw et al. 2008). Occasional directed catch or bycatch of Whale Sharks has been documented from many of their range states, particularly where large-mesh gillnets are in common use (Rowat and Brooks 2012).

Tuna are often associated with Whale Sharks, and tuna purse-seine fisheries often use Whale Sharks as an indicator of tuna presence, even setting nets around the sharks (Capietto et al. 2014). Direct mortality in purse-seine fisheries appears to generally be low, recorded as 0.91% (one of 107) and 2.56% (one of 38) of sharks where fate was reported by observers in the Atlantic and Indian Oceans, respectively (Capietto et al. 2014). However, estimated mortality rates in the Western Central Pacific purse-seine fishery were higher: 12% for 2007–2009 and 5% in 2010. This extrapolated to a total mortality of 56 sharks in 2009 and 19 in 2010 (Harley et al. 2013). Observer reports on release condition from this region from 2010–2014 were generally consistent, with 50–60% of encircled sharks released alive, 5–10% dying and 30–40% of status unknown (Clarke 2015). Assuming a poor outcome for the latter category, potential mortalities in 2014 range from a minimum of 11 to 42, with a higher number possible depending on longer-term survival of the sharks released alive (Clarke 2015). Available data on the number of Whale Sharks caught are likely to underestimate total catch (Clarke 2015). The longer-term survivorship of Whale Sharks released from nets has not been examined at this stage. Common release practices, such as being lifted or towed by the caudal peduncle, are likely to cause stress, injury and possibly death to the sharks.

Shipping lanes, where they are placed close to Whale Shark feeding areas, can create a serious risk of vessel strikes. Whale Sharks routinely feed at the surface (Motta et al. 2010, Gleiss et al. 2013), and propeller injuries are commonly recorded during monitoring programs (Rowat et al. 2006, Speed et al. 2008, Fox et al. 2013). While mortality events are seldom reported in the contemporary scientific literature, they were often noted from slower-moving vessels in the past (Gudger 1941). It is likely that fast-moving, large ships do not register or report impacts, and as Whale Sharks will typically sink upon death, these are unlikely to be documented (Speed et al. 2008). Areas where Whale Sharks appear to be at particular risk include the Mesoamerican reef countries in the Western Caribbean (Graham 2007, R. de la Parra-Venegas pers. comm.) and Gulf states (D. Robinson pers. comm.), where a high frequency of serious propeller injuries are observed during monitoring.
 
Inappropriate tourism may be an indirect threat to Whale Shark in some circumstances (for example from interference, crowding or provisioning). Marine pollution events occurring in Whale Shark hotspots, such as the Deepwater Horizon oil spill in the Gulf of Mexico in 2010 (Hoffmayer et al. 2005, McKinney et al. 2012), may result in mortality or displacement from preferred habitats. These more local threats, as well as potential future concerns such as climate change impacts (Sequiera et al. 2014), should be closely monitored.