In many animal species, alternative reproductive tactics can result in alloparenting: adult individuals providing care for juveniles that are not genetically their own progeny. In species with parental care, males may exhibit “sneaking” behavior and fertilize eggs in the nest of another male, or nesting males may commit egg theft from a more successful male, possibly to help attract females. Alloparenting may have important consequences for both male and female reproductive output and mate choice, but rates of such non-paternity in natural populations are poorly understood in many taxa, as are the ecological factors that might influence these rates. Here, we quantified the frequency of non-paternity between males and the eggs in their nests within 15 natural populations of Threespine Stickleback, and tested whether the frequency of mismatch was predicted by characteristics of the lake (lake size and nest density) or features of individual males (body size and diet) or their chosen nest location (depth and presence of vegetation). The frequency of non-paternity was relatively high across all lakes (23–66%) but was not explained by lake-level characteristics (lake area or nest density). Alloparenting was more likely for individual males with more benthic diets (as measured by stable isotopes) and for males whose nests were closer to vegetation, although this effect varied across lakes. Our results suggest that individual-level characteristics of the male and nest influence the frequency of alloparenting, and that variation among individuals and populations should be considered in studies of the genetics and evolutionary consequences of alternative reproductive tactics.