Genetically engineered fish are nearing commercialization for aquaculture. If transgenic fish escape from farms, they could encounter and interbreed with natural populations. Relative advantages of transgenic fish for fitness-related traits could drive population processes like gene flow, but fitness trait estimates will best inform risk assessments if measured under environmental conditions that are relevant to natural environments. Wild-type and growth-enhanced transgenic Japanese medakas Oryzias latipes of different genetic backgrounds were compared for the following fitness traits: fecundity, fertility, survival to sexual maturity, age at sexual maturity, and mating advantage. Because food availability and predation have been shown to alter the life histories of growth-enhanced transgenic fish, we measured traits under four different environments: (1) high food availability and no predation, (2) high food availability with simulated predation, (3) low food availability and no predation, and (4) low food availability with simulated predation. We found that regardless of environment, there was no clear fitness trend by genotype: transgenic females were more fecund than wild-type females, wild-type males obtained more matings than transgenic males, and offspring of transgenic × wild-type crosses had higher survival to sexual maturity than offspring of two wild-type parents, possibly due to heterosis. Regardless of genotype, females produced more eggs in environments with high food availability and matured fastest under conditions of high food availability and no predation. Our results imply that population-level processes like gene flow will be difficult to predict from measurements of one or two fitness traits taken on fish in a single environment. Therefore, gene flow risk assessments should be based on estimates of fitness traits that span the entire life cycle, incorporate relevant environmental variation, and compare the transgenic fish strain with a wild-type strain of relevant genetic background.