They're eutrophic (excess nutrients). In coastal systems not impacted by humans, the excess nutrients (nitrogen, phosphorous, silica) come from decaying plant matter and weathering.  However, most major estuaries have humans adding their nutrients to the mix. But there's also evidence that too much nutrients for too long can alter the community of primary producers and make it difficult to reduce excess production just by reducing nutrient inputs.  So, in general, it's excess nutrients, but it's often more complicated.  Check out the work by Carstensen on Danish systems.

http://www.aslo.net/lo/toc/vol_51/issue_1_part_2/0398.pdf

All the nutrients, minerals and organic carbon are run from catchment area of river to estuary during floods. In the estuary, it will take time to mix fresh water in to sea water due to wave action and tides, which causes estuarine water rich with  nutrients,minerals and organic carbon that promote phytoplankton  production and subsequent zooplankton production. Juveniles of many  species of fin fishes and shell fishes migrate to estuaries   to avail  rich food resource and to spend their juvenile phase as they require  brackish water during juvenile phase. Estuaries are potential areas for juvenile fisheries of fin fishes and shell fishes which have to be managed to promote recruitment to the fishery of concerned species  in the sea.

First you have to know about the definition of estuaries and its characteristics.  The tidal mouth of the big river where tides meet with the stream. Estuaries have a tidal effect resulting to the accumulation of organic and inorganic nutrients. There is natural cleaning and recycling system in all estuaries; so no possible of the degradation of nutrients.  Therefore Estuaries are by born high productive zone. Bangladesh is a land of estuaries; you can see a lot of estuaries in southern part. Some dead estuaries forms into another waterbody which name is Ox-Bow. You can find such Ox-bows in Jessore. DANIDA and World Fish worked on these water bodies.

Due to efflux of nutrients.

In addition to what was already noted, estuaries are nutrient traps because the electrochemicall interaction of fresh and salt water causes precipitation reactions (especially in the area known as the turbidity maximum).  Net non tidal drift in the the lower layer of stratified systems keeps fine sediment and nutrients recycling in the system.  Biota obviously take advantage of this, making primary and secondary  production among the highest of natural systems.

I'd underline what Weinstein wrote. The turbidity max is essential, described re physics in the attached paper. In marginal seas without essential tides but rivers entering the sea there is fluid-mud motion close to the bottom. But productivity depends, e.g. on light energy. For instance in the Yellow River, China, there is not too much light in the water due to the geology. Also, the air quality in Beijing, often mentioned as a man-made problem, has a similar turbidity due to the Gobi desert in its neighborhood. Today in Beijing all motorbikes drive on electricity, just seen 10 days ago with my own eyes. So I would guess that we cannot too much generalize the idea of highly productive estuaries.

Temperate latitude estuaries are naturally turbid, light limited, such as Delaware Bay, USA.  But productivity and production can be very high.  The standing crops of young nekton support many coastal fisheries, especially those of marine transients. 

Another factor I don't see mentioned above is the fact that shallow waters have better atmospheric oxygenation rates, so better oxygen supplies for aquatic life despite what may otherwise be an excess of nutrients leading to eutrophic conditions.

Because of the nutrient potential of estuary.

If the nutrient potential of the estuary is too (unnaturally) high, several people mentioned eutrophication, secondary production may drop (even precipitously) due to events like hypoxia and anoxia, harmful algal blooms, jellyfish predation on larval nekton, etc.  We already have too many "dead zones" due to sewage input, agricultural runoff, etc.  Don't think we want any more.