Sediments and invertebrates were sampled from 9 stormwater retention ponds (SWRPs) and 11 natural, shallow lakes in Denmark. Samples were analyzed for 13 polycyclic aromatic hydrocarbons (PAHs). The SWRPs received urban and highway runoff from various types of drainage areas and the lakes were located in areas of various land uses. Comparing PAHs in the sediments of the SWRPs and the lakes, it was found that levels of total PAH were similar in the two aquatic systems, with median values of 0.94 and 0.63 mg·(kg·DM)−1 in sediments of SWRPs and lakes, respectively. However, the SWRP sediments tended to have higher concentrations of high-molecular-weight PAHs than the lakes. A similar pattern was seen for PAHs accumulated in invertebrates where the median of total PAH was 2.8 and 2.1 mg·(kg·DM)−1 for SWRPs and lakes, respectively. Principal component analysis on the PAH distribution in the sediments and invertebrates showed that ponds receiving highway runoff clustered with lakes in forests and farmland. The same was the case for some of the ponds receiving runoff from residential areas. Overall, results showed that sediment PAH levels in all SWRPs receiving runoff from highways were similar to the levels found in some of the investigated natural, shallow lakes, as were the sediment PAH levels from some of the residential SWRPs. Furthermore, there was no systematic trend that one type of water body exceeded environmental quality standards (EQS) values more often than others. Together this indicates that at least some SWRPs can sustain an invertebrate ecosystem without the organisms experiencing higher bioaccumulation of PAHs then what is the case in shallow lakes of the same region.