Environmental DNA (eDNA) has recently emerged as a promising tool for monitoring biodiversity in aquatic systems at both the species and ecosystem level. As eDNA studies become commoner, the spectrum of methodological procedures used to capture and extract DNA from environmental samples is broadening. Inconsistent use of different protocols could result in different DNA yields and detection probabilities, hindering the comparability of studies over space and time. All workflows currently in use to analyze aquatic eDNA consist of three steps: (i) sampling a volume of water from the area of interest; (ii) a DNA capture step, concentrating the volume of the sample and; (iii) the extraction and purification of eDNA. We conducted a literature review encompassing all published aquatic eDNA studies and found a significant variation among studies in the methods used at each of these stages. In fact, we found more protocols described than there were papers published on aquatic eDNA. We also investigated the difference in DNA yield for the most commonly used methodological procedures and some recommended protocols from related fields. We included five variations on the filtration capture method, and seven different extraction protocols. Our results show a marked difference between capture methods, with both pore size and filter material used having a significant effect on DNA yield. Water type (eutrophic vs. oligotrophic) had no effect. Our data identify a clear need for the standardization of methods used in aquatic eDNA studies and we suggest an optimal methodological procedure to capture and extract marine environmental DNA.