As the Asker indicates, the difficulty is defining three differents terms in English. However, if "fonds peu profonds" actually only appears once, then "shallow waters" may suffice.

The French descriptions relate rather more to where the sea bed lies in relation to the surface, thinking from the bottom up, whereas in English, we tend to think from the surface down.

A) haut-fond
Definition from Guide des termes de marin, La Chasse-Marée : élévation du relief sous-marin, souvent dangereux pour la navigation).
This Guide suggests "shoal" in English.

Shoal : (as defined by the Oxford A-Z of Sailing Terms) : a derivative of the word “shallow”, indicating a patch of water in the sea with a depth less than that of the surrounding water. Shoals are the results of banks of sand, mud or rock on the sea bed, and are usually marked, in pilotage waters, by buoys or other sea-marks.
Shoal : (as defined by The Illustrated Dictionary of Boating terms, John Rousmaniere) : an especially shallow area of water.
“Haut fond” is used to describe shallow water where the bottom is either sand or rock.
Likewise, “shoal” seems to cover shallow water, whatever the nature of the bottom.

B) basse
i) Definition from the Dictionnaire technique maritime) : banc de rocher affleurant la surface mais ne découvrant jamais. Ce terme n’est utilisé qu’en Bretagne. Syn. haut-fond.
Examples of dive sites in Brittany : Basse Prioul, Basse des Pordicais, Basse Mélithe, but also in the Mediterranean : Basse Renette, Basse de la Moulinière. So the ter mis used in the naming of sites, an not just in Brittany, as MG has already pointed out.
ii) Definition from http://www.cnrtl.fr/definition/basse (basse 2, subst, fém) : MAR. ,,Banc de roche ou de corail s'approchant très près de la surface de la mer, mais ne découvrant jamais`` (Gruss 1952) : Certains par une longue expérience de n'y rencontrer [sur cette route marine] ni vigies ni basses, ils [les Espagnols] peuvent naviguer la nuit avec aussi peu de précautions que dans les mers d'Europe. Voyage de La Pérouse,t. 2, 1797, p. 294. Rem. Attesté dans la plupart des dict. généraux.
Prononc. Cf. basse1. Homon. basse1. Étymol. et Hist. 1484 mar. « haut-fond » (Garcie, Le Grant routier, Rouen d'apr. Arveiller dans Fr. mod., t. 25, p. 306 : il y a une basse). Substantivation du fém. de l'adj. bas*.
Given the general nature of this term and the fact that it appears to be used mainly in the naming of sites, then perhaps the term “shallows”, would be appropriate as used generally but also in site names, as with “Columbia Shallows”, Eastern Shallows” .

C) fonds peu profonds
Shallow water(s) ?

Conclusion :
haut fond = shoal
basse(s) = shallow(s)
fond peu profond = shallow water(s)