Organic-matter decomposition is a key ecosystem process in freshwater ecosystems as it influences food web dynamics, represents a considerable flux in the global carbon cycle and can provide a useful measure of the ‘health’ of freshwater habitats. While organic-matter decomposition has been well studied among lotic ecosystems, research from small standing waterbodies such as ponds is largely missing, and decomposition studies are usually conducted on a single freshwater habitat type. However, there is a need to consider ecosystem processes across multiple freshwater habitats and connected ecosystems to better characterise ecosystem functioning at the landscape-scale, given the interdependence of landscape elements. This study provides a comparative analysis of organic-matter decomposition using a standardised field assay (cotton-strip assay) in the water column, riparian zone and land zone of urban pond and stream habitats. The average daily tensile-strength loss of the cotton strips (a process that corresponds to the catabolism of cellulose by microbes) was significantly higher in the aquatic habitats than riparian and land zones when all sites were considered, and when stream and pond sites were considered separately. Furthermore, the average decomposition rate was significantly higher within the water column in river habitats compared to pond habitats, although no difference was observed among riparian and land zones. Woody debris had a negative unimodal association with average per day tensile strength loss within streams, and a positive unimodal association within pond sites. Both nitrate and shading had positive unimodal associations with average per day tensile strength loss within stream sites. Among pond habitat, urban land coverage within 250m of each site was identified to have a negative association with average per day tensile strength loss. Here we demonstrated that urban freshwater habitats have heterogeneous organic matter decomposition rates, and that the responses can be complex. Understanding key ecosystem processes at a multihabitat scale will ensure the effective inclusion of ecosystem process in freshwater assessment and conservation protocols and improve the health and resilience of urban freshwater ecosystems.