Manningtree is quite a good spot for birding. From the train recently, I suspect that the waders you saw were mainly Black-tailed Godwit, Lapwing and Redshank. It past years, a few rarities have turned up in this location, including: Long-billed Dowitcher and American Wigeon. One viewpoint over the Stour is to park at Mistley Walls, just east of Manningtree, and view from there. My suggestion, however, would be to park at the Coop in Manningtree and walk west along the seawall. After passing under the railway line, you come to a marshy area on your left called The Splodge, which is often one of the first places in Essex to have spring arrivals of Little Ringed Plover. Soon after that, cross the road and continue on the riverside path all the way to Flatford Mill. Again, this might be more productive of birds in Spiring, but it is a nice walk. Some way along the path, you can look over to the lagoons north of the river (a scope is handy) where Garganey regularly turn up in Spring.
This info is fantastic thanks. I visited the Tate galleries whilst in London and inspired by constable I am definitely interested in the Flatford area too. I will be travelling by train and wondered if you had any tips for a route to take in the Stour estuary and Flatford, incorporating birding?
There's a main footpath leading from the train station carpark that passes under the railway line and out to Flatford which is pretty good for birds like Cuckoos and Sedge/Reed Warblers (should also be a good area for Barn Owls but I've never been there in the evening/early morning to confirm it) but the main bird interest is probably more out along around Manningtree and east along the estuary. Following the A137 north of Manningtree to the Stour you can see waders there (Greenshanks and the like) and I think there's a hide in that area but whether it's public access I couldn't say. The estuary around Manningtree town is definitely a great spot for general birdwatching though, always lots of waders and wildfowl in the area.