Relatively little information is available on environmental associations and the conservation of Odonata in the Maltese Islands. Aquatic habitats are normally spatio-temporally restricted, often located within predominantly rural landscapes, and are thereby susceptible to farmland water management practices, which may create additional pressure on water resources. This study investigates how odonate assemblage structure and diversity are associated with habitat variables of local breeding habitats and the surrounding agricultural landscapes. Standardized survey methodology for adult Odonata involved periodical counts over selected water-bodies (valley systems, semi-natural ponds, constructed agricultural reservoirs). Habitat variables relating to the type of water body, the floristic and physiognomic characteristics of vegetation, and the composition of the surrounding landscape, were studied and analyzed through a multivariate approach. Overall, odonate diversity was associated with a range of factors across multiple spatial scales, and was found to vary with time. Lentic water-bodies are probably of high conservation value, given that larval stages were mainly associated with this habitat category, and that all species were recorded in the adult stage in this habitat type. Comparatively, lentic and lotic seminatural waterbodies were more diverse than agricultural reservoirs and brackish habitats. Overall, different odonate groups were associated with different vegetation life-forms and height categories. The presence of the great reed, Arundo donax L., an invasive alien species that forms dense stands along several water-bodies within the Islands, seems to influence the abundance and/or occurrence of a number of species. At the landscape scale, roads and other ecologically disturbed ground, surface water-bodies, and landscape diversity were associated with particular components of the odonate assemblages. Findings from this study have several implications for the use of Odonata as biological indicators, and for current trends with respect to odonate diversity conservation within the Maltese Islands.