Thirty percent of the flower flies (Diptera: Syrphidae) diversity is concentrated in the Neotropics, with few studies in the Amazonian rainforests. We evaluated diversity, phenology and bait preference of Syrphids along an environmental gradient, including forest edge (FE), dense secondary forest (DFS) and agroforestry system (AFS). Adults were collected using Van Someren-Rydon traps (VSRTs) baited with fermented fruit, decomposed shrimp and fish. We sampled nine days per climatic season (high, HIR and low rainfall intensity, LIR), including nine sampling points per habitat in the Reserva Natural y Ecoturística La Avispa, Caquetá, Colombia. We estimated alpha and beta diversity components within and between habitats. Phenology was compared between climatic seasons. 1.379 specimens were collected, belonging to 59 species (13 genera). DFS had the higher abundance and richness (n = 812; 43 species), suggesting that conserved habitats offer a wide range of resources. Abundance during HIR was 8.9 times higher (n = 1.240), while richness was 1.8 times higher (68 species) than LIR, suggesting that rainfall influences diversity. An example is the high abundance and diversity of Copestylum (n = 1.225; 61.1%) which breeds in phytotelmata, indicating high availability of these microhabitats. The VSRTs showed high sampling completeness (≥ 90%), suggesting that this methodology is useful for rapid Syrphids inventories, however the lack of typical Amazonian groups evidences the need to use complementary methods. Species replacement was the dominant component of betadiversity, indicating that each habitat contributes with unique species, providing functions for sustainability and ecosystem balance, where connectivity is essential to ensure the provision of the services in undergoing ecological restoration areas, such as the tropical rainforest studied here.