We examined methylmercury (MeHg) bioavailability in four of the most predominant wetland habitats in California's Central Valley agricultural region during the spring and summer: white rice, wild rice, permanent wetlands, and shallowly-flooded fallow fields. We sampled MeHg and total mercury (THg) concentrations in two aquatic macroinvertebrate taxa at the inlets, centers, and outlets of four replicated wetland habitats (8 wetlands total) during two time periods bounding the rice growing season and corresponding to flood-up and pre-harvest (96 total samples). In general, THg concentrations (mean ± standard error) in Notonectidae (Notonecta, back swimmers; 1.18 ± 0.08 µg g^− 1 dry weight [dw]) were higher than in Corixidae (Corisella, water boatmen; 0.89 ± 0.06 µg g^− 1 dw, MeHg: 0.74 ± 0.05 µg g^− 1 dw). MeHg concentrations were correlated with THg concentrations in Corixidae (R² = 0.80) and 88% of THg was in the MeHg form. Wetland habitat type had an important influence on THg concentrations in aquatic invertebrates, but this effect depended on the sampling time period and taxa. In particular, THg concentrations in Notonectidae, but not Corixidae, were higher in permanent wetlands than in white rice, wild rice, or shallowly-flooded fallow fields. THg concentrations in Notonectidae were higher at the end of the rice growing season than near the time of flood-up, whereas THg concentrations in Corixidae did not differ between time periods. The effect of wetland habitat type was more prevalent near the end of the rice growing season, when Notonectidae THg concentrations were highest in permanent wetlands. Additionally, invertebrate THg concentrations were higher at water outlets than at inlets of wetlands. Our results indicate that although invertebrate THg concentrations increased from the time of flood-up to draw-down of wetlands, temporarily flooded habitats such as white rice, wild rice, and shallowly-flooded fallow fields did not have higher THg or MeHg concentrations in invertebrates than permanent wetlands.