This study was conducted to determine the levels of selected heavy metals in the muscle tissue of Metapenaeus dobsoni and Penaeus indicus shrimp species from Negombo and Puttalam lagoons in Sri Lanka to compare heavy metal levels in shrimp species between two lagoons and evaluate potential risks to human health associated with shrimp consumption. Samples were collected monthly from October 2022 to March 2023 and quantified for Cu and Zn using FAAS, while Cr using GFAAS. The mean heavy metal levels in µg/g wet weight in the Metapenaeus dobsoni captured from Negombo lagoon were found in order of Cu (4.1±1.7) > Zn (4.0±3.3) > Cr (0.061±0.031), while captured from Puttalam lagoon were found in order of Zn (6.6±4.3) > Cu (6.6±1.4) > Cr (0.076±0.005). The mean metal levels in µg/g wet weight found in Penaeus indicus were as follows, Cu (4.4±1.8) > Zn (2.7±1.3) > Cr (0.048±0.019) in Negombo lagoon and Cu (5.9±0.8) > Zn (4.4±2.3) > Cr (0.073±0.030) in Puttalam lagoon. The findings show that the heavy metals levels detected in shrimp samples were generally higher in Puttalam Lagoon than in Negombo Lagoon. In addition, the results demonstrated that shrimp from both lagoons and species were safe for human consumption during the study period since none of the heavy metal levels in the shrimp samples exceeded the maximum permissible level allowed for shrimp consumption according to FAO/WHO. Furthermore, THQ values indicated that there was no non-carcinogenic risk of the determined metals via the consumption of these shrimp species captured from both lagoons.