Abstract Background Environmental factors such as temperature, rainfall, and vegetation cover play a critical role in malaria transmission. However, quantifying the relationships between environmental factors and measures of disease burden relevant for public health can be complex as effects are often non-linear and subject to temporal lags between when changes in environmental factors lead to changes in the incidence of symptomatic malaria. The study aim was to investigate the associations between environmental covariates and malaria incidence in high transmission settings of Uganda.Methods This study leveraged data from seven malaria reference centres (MRCs) located in high transmission settings of Uganda over a 24-month period (January 2019 - December 2020). Estimates of monthly malaria incidence (MI) were derived from MRCs’ catchment areas. Environmental data including monthy average measures of temperature, rainfall, and normalized difference vegetation index (NDVI) were obtained from remote sensing sources. A distributed non-linear lagged model was used to investigate the quantitative relationship between environmental covariates and malaria incidence. Results Overall, the median (range) monthly temperature was 30oC (26-47), rainfall 133.0 mm (3.0-247), NDVI 0.66 (0.24-0.80) and MI was 790 per 1000 person-years (73-3973). A non-linear relationship between environmental covariates and malaria incidence was observed. An average monthly temperature of 35oC was associated with significant increases in malaria incidence compared to the median observed temperature (30oC) at month lag 2 (IRR: 2.00, 95% CI: 1.42-2.83) and the cumulative increases in MI significantly at month lags 1-4, with the highest cumulative IRR of 8.16 (95% CI: 3.41-20.26) at lag month 4. An average monthly rainfall of 200mm was associated with significant increases in malaria incidence compared to the median observed rainfall (133mm) at lag month 0 (IRR: 1.24, 95% CI: 1.01-1.52) and the cumulative IRR increases of malaria at month lags 1-4, with the highest cumulative IRR of 1.99(95% CI: 1.22-2.27) at lag month 4. An average NVDI of 0.72 was associated with significant cumulative increases in IRR of malaria as compared to the median observed NDVI (0.66) at month lag 2-4, with the highest cumulative IRR of 1.57(95% CI: 1.09-2.25) at lag month 4. The rate of increase in cumulative IRR of malaria was highest within lag months 1-2 as compared to lag months 3-4 for all the environmental covariates.Conclusions In high-malaria transmission settings, high values of environmental covariates were associated with cumulative increases in the incidence of malaria, with peak associations occurring after variable lag times. The complex associations identified are valuable for designing strategies for early warning, prevention, and control of seasonal malaria surges and epidemics.