The application of manure and sewage sludge on farmland is a crucial element in enhancing soil organic matter and contributing to soil carbon sequestration. However, these organic fertilizers are often contaminated with anthropogenic pollutants that can harm ecosystems and persist for extended periods. Bioremediation approaches have gained attention as a cleanup treatment in recent decades due to their cost-effectiveness and environmental friendliness. In addition to phytoremediation and bacterial bioremediation, mycoremediation has also proven successful in pollution control. While land-based fungal species, particularly white-rot fungi, have been extensively studied for mycoremediation, marine fungi are underrepresented but possess adaptive traits (e.g., halophilic, anaerobic) that could be beneficial under specific conditions, potentially expanding the degradation portfolio. In an initial step, marine filamentous fungi from the Flensburg strain collection of marine fungi were screened in a simple growth medium for their ability to tolerate and metabolize the analgesic diclofenac (DCF), a substance regularly detected in surface waters that is toxic to various organisms. The cultivation period lasted 28 days. Of the 40 isolates tested, 6 exhibited almost no metabolization, 20 showed a mediocre degradation, and 14 had a residual concentration of DCF at 15% and below. These results demonstrate the capability of some marine fungi to metabolize DCF. The second pollutant to be tested is perfluorooctanoic acid (PFOA), representing the group of per- and polyfluoroalkyl substances (PFAS), which are also harmful and ubiquitously found in the environment. In the final step, selected fungal candidates will be employed to degrade these organic contaminants in manure and sewage sludge. The degradation rate and products will be assessed using LC-MS, with kinetics determined. This study provides an example of an applied bioremediation technique as a sustainable, eco-friendly, and inexpensive way to deal with pollutants, thereby promoting the use of organic fertilizers in agriculture to scale up soil carbon sequestration.