Malaria is a vector-borne disease of significant public health concern. Despite widespread success of many elimination initiatives, elimination efforts in some regions of the world have stalled. Barriers to malaria elimination include climate and land use changes, such as warming temperatures and urbanization, which can alter mosquito habitats. Socioeconomic factors, such as political instability and regional migration, also threaten elimination goals. This is particularly relevant in areas where local elimination has been achieved and consequently surveillance and control efforts are dwindling and are no longer a priority. Understanding how environmental change, impacts malaria elimination has important practical implications for vector control and disease surveillance strategies. It is important to consider climate change when monitoring the threat of malaria resurgence due to socioeconomic influences. However, there is limited assessment of how the combination of climate variation, interventions and socioeconomic pressures influence long-term trends in malaria transmission and elimination efforts. In this study, we used Bayesian hierarchical mixed models and malaria case data for a 29-year period to disentangle the impacts of climate variation and malaria control efforts on malaria risk in the Ecuadorian province of El Oro, which achieved local elimination in 2011. We found shifting patterns of malaria between rural and urban areas, with a relative increase of Plasmodium vivax in urbanized areas. Minimum temperature was an important driver of malaria seasonality and the association between warmer minimum temperatures and malaria incidence was greater for Plasmodium falciparum compared to P. vivax malaria. There was considerable heterogeneity in the impact of three chemical vector control measures on both P. falciparum and P. vivax malaria. We found statistically significant associations between two of the three measures [indoor residual spraying (IRS) and space spraying] and a reduction in malaria incidence, which varied between malaria type. We also found environmental suitability for malaria transmission is increasing in El Oro, which could limit future elimination efforts if malaria is allowed to re-establish. Our findings have important implications for understanding environmental obstacles to malaria elimination and highlights the importance of designing and sustaining elimination efforts in areas that remain vulnerable to resurgence.