Slight departures from bilateral symmetry are usually associated with reduced fitness. Here we show that an insular freshwater population of Gasterosteus aculeatus exhibits spatial and temporal segregation according to the incidence and direction of asymmetry in the number of bony lateral plates, which are important predator-defense structures. We analyzed 11,263 fish collected from 19 full lake transects over three years, and found that signed asymmetries for plate number were slightly left-side biased. Asymmetries occurred in 55% of the stickleback with more asymmetrics found during cold weather, and more left-biased individuals found during windy conditions, possibly due to environmentally driven activity levels that differ among asymmetric forms. Absolute plate asymmetries were randomly distributed in the lake, but there was a strong shift in signed plate asymmetry from a mean of zero in littoral zones to left-side bias in limnetic zones, probably due to microhabitat choices among asymmetric forms. Video data of avian piscivores on the lake show laterality in prey handling, providing a potential mechanism for asymmetric prey morphology. Our results imply a complex relationship between slight asymmetries and niche space that is relevant to the broader literature on the evolutionary implications of developmental instability and intrapopulation variability.