These kits provide a convenient and rapid method for the isolation of microorganisms from water samples. The kits allows for the rapid isolation and purification of total RNA and DNA simultaneously from the microorganisms found in different types of water samples. The total RNA and DNA (including genomic DNA) are isolated from all the microorganisms found in the water, including bacteria, fungi and algae without the use of any inhibitory organic substances. The kit purifies genomic DNA, and all sizes of RNA, from large mRNA and ribosomal RNA down to microRNA (miRNA) and small interfering RNA (siRNA). The purified RNA and DNA are highly concentrated, and can be used directly in a number of downstream applications including PCR, qPCR, RT-PCR, qRT-PCR, Northern blotting, Southern blotting and sequencing reactions.