Surface enhanced Raman spectroscopy (SERS) has been widely applied for rapid and sensitive detection of various chemical and biological targets. Here, we incorporated a syringe filter system into the SERS method to detect pesticides, protein toxins and bacteria in water. For the detection of chemical and protein targets, silver nanoparticles (Ag NPs) were aggregated by sodium chloride (NaCl) to form nanoclusters that could be trapped in the pores of the filter membrane to from the SERS-active membrane. Then a coating of capture (e.g. aptamer) was integrated on the nanoparticle substrate if needed. Then samples were filtered through the membrane. After capturing the target, the membrane was taken out and air dried before measuring by a Raman instrument. The developed filter SERS method was able to detect fungicide ferbam as low as 2.5 ppb level and had a good quantitative capability, which could also be carried out on site using a portable Raman instrument. The aptamer integrated filter SERS was able to detect ricin b chain in water at 100 ppb level. The filter membrane was then applied to detect bacteria E.Coli with the integration of 4-mpba as a capture and indicator. With SERS mapping, we can detect E.Coli down to 101 CFU/ml and the viability of bacteria on the membrane could be confirmed by incubating the membrane on TS agar down to 102 CFU/ml. This study shows the filter based SERS methods improve the detection capability in water samples, with a great versatility for various types of assays.