Serious concerns have arisen regarding urbanization processes in western Amazônia, which result in the creation of artificial habitats, promoting the colonization of malaria vectors. We used structural equation modelling to investigate direct and indirect effects of forest cover on larval habitats and anopheline assemblages in different seasons. We found 3474 larvae in the dry season and 6603 in the rainy season, totalling ten species and confirming the presence of malaria vectors across all sites. Forest cover had direct and indirect (through limnological variables) effects on the composition of larval anopheline assemblages in the rainy season. However, during the dry season, forest cover directly affected larval distribution and habitat variables (with no indirect affects). Additionally, artificial larval habitats promote ideal conditions for malaria vectors in Amazonia, mainly during the rainy season, with positive consequences for anopheline assemblages. Therefore, the application of integrated management can be carried out during both seasons. However, we suggest that the dry season is the optimal time because larval habitats are more limited, smaller in volume and more accessible for applying vector control techniques.