Classic models of apparent competition predict negative indirect effects between prey with a shared enemy. If predator per capita growth rates are nonlinear, then endogenously generated periodic cycles are predicted to generate less negative or even positive indirect effects between prey. Here I determine how exogenous mechanisms such as environmental variation could modify indirect effects. I find that exogenous variation can have a broader range of effects on indirect interactions than endogenously generated cycles. Indirect effects are altered by environmental variation even in simple models for which the per capita growth rate of the predator species is a linear function of population densities. Temporal variation that affects the predator attack rate or the conversion efficiency can lead to large increases or decreases in the indirect effects between prey, dependent on how prey populations co-vary with the environmental variation. Positive indirect effects can occur when the period of environmental variation is close to the natural period of the biological system and shifts in subharmonic resonance occur with the addition of the second prey. Models that include nonlinear numerical responses generally lead to indirect effects that are sensitive to environmental variation in more parameters and across a wider range of frequencies.