The main sources of coastal pollution are:

1. Direct Discharge – primarily from municipal and industrial wastewater from coastal cities & industrial parks; and

2. Indirect Transportation by Rivers to the Sea – rivers carry heavy metals discharged upstream into coastal waters

amounts carried by rivers to sea are hundreds & thousand times higher and rising.

In recent years, although the direct discharges have been controlled and are declining, heavy metal discharge delivered by the rivers remain significant. It is clear that direct discharge is negligible when compared to the amount of heavy metal carried by the rivers to the sea.

it is easier to control discharge pipes and big industrial enterprises & parks along the coastline than dispersed polluting SMEs along rivers across.

we need to start tackling pollution at source so as to control and reduce amounts carried by rivers to the sea to allay increasing fears over heavy metal pollution in seafood.

http://chinawaterrisk.org/opinions/chinas-coast-the-unbearable-weight-of-heavy-metal-pollution/

Minimization and checking at the source are two major methods. 

Any method in sea water is not 100% efficient for metal removal. 

It keeps generating like a cycle independent of methods you follow to treat.  If the concentration is too high then go for adsorbents  

Coastal water means either fresh water aquifer or saline water. Some time interface boundaries are also found. It is necessary to have detailed chemical quality of waters. Identify the pollutants and their concentration. For removal/ minimize  of metalic pollutants this may not be a uniform/common  process but  depend on one pollutant to other. For this well planned study which include monitoring of water samples and their chemical analysis is required. From this further study can be evaluated.

The best, easy and cost-effective way is the treatment of metal containing discharges at source or near an Industrial Zone at the start of main drain. This will save whole of the soil-water-plant - human -animal system from metals.

Irrespective of the source of pollution, prevention is the best policy. Otherwise, treating or minimizing at or near the source would be the next option. Once they get into the coastal ecosystem, they disperse, transform, etc. so reduction can become very challenging and expensive. 

Apart from prevention and treating the waste water.., I think the best and most natural way can be phytorremediation, but in fact it could be a diffcult, long process

Many studies have been carried to elucidate the molecular basis for metal accumulation, which can provide a scientific basis to outline several strategies for phytoremediation of metals. 

Conference Paper Phytoremediation of heavy metals from coastal waters and the...

Chapter Molecular Mechanisms in the Phytoremediation of Heavy Metals...

Simply do in on source:

Application of pre-treatment processes of industrial and domestic waste water before discharge into the marine environment

Everything carried out by Rivers ultimately ended into the marine environment which have a great contribution of heavy metals in Seas (Reduce contamination of fresh water also)

Good luck

This is a difficult task in places where there is no central sewerage system. In such places, erosion could carry metals from industries, municipalities, open waste dumps, automobile repairing sites, agricultural fields and many other point and non-point sources. Reduction of metals into coastal water therefore starts from the source, and proper treatment of waste water and effluent discharges from their point of generation.