If your aquarium is intended to model the local environment a flow
through system can have some real advantages:
1. Water temperature - Handled (assuming that there isn't too long a
run from the shore to your tank)
2. Water chemistry - Handled
3. Plankton for any suspension feeders - Handled
There are, however, some pretty serious potential problems as well.
1. Recruitment - The intake piping is an absolutely heavenly
environment for all manner of suspension feeders. The system that I'm
involved with needs to be cleaned or replaced several times per year
because it gets 90% clogged by worms, barnacles, mussels, etc. This is
in spite of the fact that we actually have two intakes that are
alternated monthly in order to kill off the clogging animals.
2. Gunk - There's a lot of microscopic stuff that will come into your
system and then settle out. Left unattended, your rockwork would
almost constantly look 'dusty'. That problem is pretty easy to deal
with but it does require attention at least weekly.
3. Catastrophes - Depending on where your intake is and what is going
on in the area, things can go very wrong almost instantly. Several
years ago the local port authority authorized some dredging adjacent
to our intake. The resulting turbidity killed virtually every animal
in the facility. We've also had two or three instances of storms
coming in from unusual directions that also caused excess turbidity
and 10 to 30% mortality.
4. Pumping capacity - The distance from intake to tank will make an
absolutely huge difference in the size of the pump you need. I don't
have exact figures but based on my experience pumping various
materials I think that doubling the length of the run will require
quadrupling the size of the pump in order to maintain the same flow
rate. BTW: This and the recruitment problem both argue in favor of the
largest diameter pipe you can handle.
There is no hard and fast rule about where to draw your water.
Obviously, you want clean water but that doesn't necessarily mean that
you have to go far offshore. Your best bet is to look at where your
intake might be located and then compare what lives there to what
lives in areas that you consider to be pristine. The water depth at
the intake site can be pretty important. If you can draw your water
from a spot where the depth is at least double the maximum expected
wave height (3 or 4 times would be better) you'll reduce the chances
of a catastrophic turbidity event.
Screening your intake is useful for keeping drift algae out of the
system but won't do a thing about recruitment (remember that these
little guys come in as almost microscopic larvae). You would want the
screen area to be as large as possible to prevent stuff from being
sucked onto and clogging it. I think you would get good results with a
200L plastic drum with numerous large diameter holes cut into it and
then screened over.
In the final analysis, I suspect that there are vanishingly few
situations where a flow through home aquarium is practical.