I think you will have any length of DNA in the water, but as smaller the fragment get you will catch more species. So it is mostly a compromise between how long it should be to answer my question but get a maximum of species. Theseis always depending on your question as well as the ecosystem, leads to the normal final conflict of Biodiversity against specifity.

I working in marine water with 120-170 bp and try to be less than 200bp and I have good experience with that. So it should also work for aquatic system, mostly even better. But the problem is more that DNA degenerated differently, even within mitochondrial DNA I suggest large differences between regions based on my results.  

 Hope these give any helpful information to you!

Thank you for your response. Encouraged to know that eDNA fragments can be of a considerable size! 

Amplicons ranging from as small as 62 bp (Foote et al. 2012) to as large as 650 bp (Foote et al. 2012; Egan et al. 2013) have proved successful at eDNA detection

for aquatic sampling, although most currently published papers have aimed for fragment sizes of less than 150bp (e.g. Dejean et al. 2012; Takahara et al. 2012; Wilcox et al. 2013).

However, recent studies do suggest that as long as you aim for relatively small fragment sizes (say under 250bp), amplicon size likely has little effect on amplification. 

Check out this recent paper for more details and references therein:

https://www.researchgate.net/publication/307144783_Characterization_optimization_and_validation_of_environmental_DNA_eDNA_markers_to_detect_an_endangered_aquatic_mammal

DOI: 10.1007/s12686-016-0597-9

Article Characterization, optimization, and validation of environmen...

Thanks Kathryn