Calliphoridae and Mesembrinellidae are relevant to environmental conservation, public health, and forensic entomology. Researches regarding the flight behavior and the influence of abiotic factors on these insects may assist the application of entomology sciences. This study aimed to analyze the population fluctuation of Calliphoridae and Mesembrinellidae, verifying the influence of environmental factors, trap height, and the anthropic effect in the Itaipu–Piratininga lagoon complex, Niterói (RJ). The collections were carried out monthly from September 2015 to August 2016, with fish bait (sardines) exposed for 48 h, totaling six traps, installed in three physiognomies (mangrove, ombrophilous forest, and restinga) at 1.5 and 2.5 m from the ground. Nine thousand seven hundred seventy-three individuals were captured, comprising two families, five genera and 11 species. Chrysomya megacephala (Fabricius, 1794) (Diptera: Calliphoridae) was the predominant species and Mesembrinella bellardiana (Aldrich, 1922) (Diptera: Mesembrinellidae) the least representative, indicating the low preservation level of this ecosystem. There was a weak, positive correlation between abundance of Chloroprocta idioidea (Robineau Desvoidy, 1830) (Diptera: Calliphoridae), Ch. megacephala, Chrysomya putoria (Wiedemann, 1818) (Diptera: Calliphoridae), and Lucilia cuprina (Wiedemann, 1830) (Diptera: Calliphoridae) with the temperature, as well as between the abundance of C. idioidea and Chrysomya albiceps (Wiedemann, 1819) (Diptera: Calliphoridae) with precipitation; however, there was no correlation between abundance and relative humidity. No significant influence of the trap height was observed. We stated a high influence of anthropic effects on the restinga and mangrove physiognomies, while the forest physiognomy still retains its preserved characteristics, with the dominance of forestall species.