FISH BIOECOLOGY IN RELATION TO SEDIMENTS

IN THE MEKONG AND IN TROPICAL RIVERS

BARAN Eric, GUERIN Eric

Project

“A Climate Resilient Mekong: Maintaining the Flows that Nourish Life”

led by the Natural Heritage Institute

March 2012
2

Table of content

1 INTRODUCTION ........................................................................................................................5

2 SEDIMENTS: CORE NOTIONS ....................................................................................................7

2.1 Sediment particle size.......................................................................................................8

2.2 Sediments and organic matter.......................................................................................11

2.3 Sediments and inorganic matter....................................................................................12

2.4 Sediment loads...............................................................................................................13

3 MEKONG FISH: CORE NOTIONS..............................................................................................15

4 SEDIMENTS AND FISH BIOECOLOGY.......................................................................................17

4.1 Sediments and fish respiration.......................................................................................17

4.2 Sediments and fish nutrition ..........................................................................................19

4.3 Sediments and reproduction..........................................................................................22

4.4 Sediments and migration ...............................................................................................29

4.5 Sediments and fish habitat.............................................................................................30

5 SEDIMENTS AND FISH PRODUCTION......................................................................................36

6 CONCLUSIONS.........................................................................................................................39

7 BIBLIOGRAPHY ........................................................................................................................41

Citation

Baran E. and Guerin E. 2012 Fish bioecology in relation to sediments in the Mekong and in 

tropical rivers. Report for the Project “A Climate Resilient Mekong: Maintaining the Flows that 

Nourish Life” led by the Natural Heritage Institute. WorldFish Center, Phnom Penh, Cambodia.

Acknowledgements

We sincerely thank Saray Samadee for her overall assistance, in particular with the literature 

(gathering, referencing, checking), Yivchhoy Chhuong for illustrating this report (cover and 

figures 4 and 10) and Chris Myschowoda for editing it.
3

EXECUTIVE SUMMARY

The Mekong Basin is experiencing rapid development, including plans for the construction of 88 

hydropower projects by 2030, which will have a very substantial impact on the river’s sediment 

load (sediment trapping by dams). The current report reviews the interactions between 

sediments and fish in tropical rivers and in the Mekong, and focuses more specifically on a 

reduction of sediment loads following dam construction.

In the Mekong, the total annual sediment discharge is about 160 million tonnes per year on 

average, with a wide range of intra-annual as well as inter-annual variability. Sediments in rivers 

are found in two main forms (suspended and bedded sediments) and they consist of a variety 

of particle sizes (roughly categorized as gravel, sand, clay and silt). Most of the sediment load in 

the Mekong is suspended. 

One property of sediments is that they adsorb and thus facilitate the transport of nutrients (in 

particular phosphorus and nitrogen) and organic particles. As dissolved nutrients in the water 

are generally low, the main nutrient load is associated with sediments. The dominant sediment 

categories in the Lower Mekong Basin are fine sands, silts and clays; the proportion of organic 

particles represents 6-8% of the total sediment load, which is considered high by global 

standards.

The Mekong is a place of exceptional fish biodiversity. Fish biodiversity increases downstream 

and the 3S system is a hotspot. The Mekong produces about 18% of the world’s freshwater fish 

yield. Mekong fish resources are essential to food security in the basin. Fish migrations are an 

essential feature of the Mekong. Sediments influence fishes’ biological functions, particularly 

respiration, nutrition, reproduction and migration, but also their habitat. Nutrient load is also a 

dominant factor explaining the overall productivity of tropical river ecosystems (including 

floodplains, estuaries and coastal areas).

Respiration. The organic component of sediments has a direct negative impact on dissolved 

oxygen through its Oxygen Demand. Suspended sediments and adsorbed nutrients also 

influence the amount of dissolved oxygen in the water through their interference with plant 

photosynthesis. 

Nutrition. Sediments are the basic input for the food chains and trophic webs that fish are part 

of at a higher level, and thus are an essential component of fish nutrition. Suspended sediments 

and the turbidity they cause reduce photosynthesis and thus decrease primary production. 

Suspended sediments also play a role in predator-prey relationships. In the Mekong, a 

reduction of sediment loads is likely to result in decreased primary production, which might in 

turn change the dominant fish species and drive down fish productivity. But the relative 

influence of nutrients loads and turbidity on primary production must be clarified for this 

potential impact to be assessed. 
4

Reproduction. The main relationship between fish reproduction and sediments is through 

spawning grounds. In estuaries high turbidity is favorable to the larvae of many coastal fish 

species. There is little information in the literature about the relationship between tropical fish 

reproduction and the impact of a reduced sediment load.

Migrations. Changes in turbidity or water color are a migration trigger for at least nine of the 

migratory species in the Mekong. Fish migrations can play a significant role in the nutrient 

distribution in the river basin. In the Mekong fish constitute a nutrient transfer from nutrientrich downstream floodplains towards more oligotrophic upstream tributaries.

Habitat. Sediment load plays a major role in river geomorphology and in the riverbed and 

riverine habitats. Blocking sediment load will degrade the river bed downstream and will 

therefore affect the aquatic organism communities adapted to these specific habitats. In the 

Mekong, deep pools, an essential habitat for the survival of numerous fish species during the 

dry season, could be affected by modified water flows that result in an infilling of these pools, 

though this impact remains to be clarified. Water pH is also a characteristic of fish habitats that 

is related to suspended sediment concentrations.

The river flood pulse concept explains the exceptionally high productivity of rivers and their 

associated floodplains. It has been widely accepted as describing the exceptional productivity of 

the Mekong. Dam development is expected to reduce `the flood pulse as well as downstream 

sediment concentrations; this combination may have a synergetic and negative effect on the 

overall productivity of the river downstream, leading to its oligotrophication. This process of 

nutrient rarefaction, poorly studied, changes food web structures and decreases fisheries 

resources. Oligotrophication is most commonly related to phosphorus deficiency, but the 

nitrogen/phosphorus ratio is also to be considered. Ongoing hydrodynamic and physical 

modelling will also clarify the retention rate of dams and the fate of sediments, but the 

coupling between sediments and nutrients and the role of the amount of nutrients that are 

independent of sediments remain to be addressed.
5

1 INTRODUCTION

Sediments are an essential component of rivers and of their biological functioning. In addition 

to their influence on river geomorphology (maintenance of river forms and habitats such as 

pools and sand bars), sediments also include nutrients, detritus and organic debris of various 

sizes which interact with the river’s different life forms, including fish (USEPA, 2003). The 

interaction between sediments and aquatic organisms, directly or indirectly through the effects 

of sediments on physical habitats, unquestionably influences the biodiversity and productivity 

of a river.

The Mekong is the second river in the world after the Ganges for its load in suspended solids1

, 

and is also the second richest river in the world in terms of fish biodiversity (Carling 2009; 

Baran 2010). Its average sediment discharge is estimated at 160 million tonnes per year, i.e. 

12% more than the Amazon River (Wolanski and Nguyen Huu Nhan 2005, Sarkkula et al. 2010). 

The Mekong Basin is experiencing rapid development, including plans for the construction of 

88 hydropower dams by 2030, which will have a very substantial impact on the river’s 

sediment load: when river flows enter a dam reservoir they decrease in velocity, which results 

in a fraction of the transported sediment being deposited in the dam reservoir (Palmieri et al. 

2003, Lu and Siew 2005, and Figure 1). Thus, the Strategic Assessment of Mekong mainstream 

dams predicts a 75% reduction of the sediment load at the mouth of the Mekong by 2030 if all 

planned dams are built (ICEM 2010). 

Figure 1: Accumulation of sediment behind dams. Source: Fruchart 2009

An abundant literature covers the effects of increased sediment and nutrient concentrations 

caused by reservoir sediment flushing or organic pollution on fish; however, very few studies 

detail the consequences of reduced sediments or nutrients for fish communities and 

production. This might be explained by visibility and timing issues: while flushing operations are 

spectacular and their impact immediately measurable, the effects of reduced sediment loads 

on ecosystems involve long-term processes such as modification of the river morphology over 

 

1 These figures are somewhat disputed since Welcomme (1985) indicates 190 and 406 million tonnes of suspended 

load for the Mekong and the Amazon respectively, but 560, 812 and 1625 million tonnes for the Yangtze, 

Brahmaputra and the Ganges respectively. The Yangtze, Brahmaputra and Amazon are not part of Carling’s 

comparison.
6

decades (as a consequence of sediment loss) and oligotrophication (resulting from nutrient 

loss) whose impacts on fish communities are gradual, over several years. The consequences of 

these processes might also be buffered and thus hidden for a while by the resilience capacity of 

the river (nutrients released by the floodplain and sediments released by erosion to overcome 

the losses in upstream inputs).

TEXT BOX 1

MRC State of the Basin report, 2003 (excerpts)

At present the MRC monitors chemical water quality once or twice per month at 98 sites. Sampling has 

been conducted since 1985 in three LMB countries, and since 1992 in Cambodia. The data collected 

under the MRC sampling programme are taken just below the water surface, and give no indication of 

the bedload transport of sediment. Nevertheless, the measure should act as a reasonable indicator of 

the amount of sediment in the water.

The concentrations of TSS showed a decrease at 23 sites and an increase at six. Notable regions where 

TSS concentrations decreased were the entire set of Mekong mainstream sites between Chiang Saen 

and Pakse in Lao PDR, and eight of the 13 sites in northeastern Thailand. The trends in phosphorus and 

nitrogen were similar [except in the Delta]..

The most prominent change at mainstream sites was the decrease in TSS which extended from Chiang 

Saen downstream. At the Chiang Saen site, the decline in TSS concentrations is likely to be due to 

changes that have occurred in China. The most likely dam that could have influenced the river is the 

Manwan Dam. Regression analyses on data before and after the dam started filling in 1992 demonstrate 

that the decrease in TSS in the downstream sites has been caused by the entrapment of suspended 

sediment by the dam.

Figure: Suspended solids concentrations in the Mekong River at Chiang Saen, with linear regression lines fitted 

for the periods before and after the Manwan Dam commenced filling in 1992
7

The current report reviews the interactions between sediments and fish in tropical rivers and 

in the Mekong, and focuses more specifically on a reduction of sediment loads following dam 

construction. Sediment loads increase due to reservoir flushing and the impact of flushing on 

fishes are reviewed in another report (Reservoir sediment flushing and fish resources). The 

second and third sections of the present report (respectively “Sediments” and “Mekong fish”) 

introduce some core notions related to sediments and fish in the Mekong. In Section 4

(“Sediments and fish bioecology”) we review the interactions between sediments and i) fish 

biological functions (respiration, reproduction, etc.) and ii) fish habitat (biotope and water 

quality). In sections 5 the role of sediments in fish productivity is reviewed, before reviewing in 

the conclusion the main findings and knowledge gaps identified.

2 SEDIMENTS: CORE NOTIONS

Sediments in rivers are found in two main forms: suspended and bedded sediments (SABS). 

This distinction is based on the sediments’ size, nature and mode of transportation by the 

water. Suspended sediments are made of “particulate organic and inorganic matter that 

suspend in or are carried by the water” while bedded sediments or bedload “accumulate in a 

loose, unconsolidated form on the bottom of natural water bodies” (USEPA, 2003)2. Thus, 

coarse material, gravel and pebbles are transported by the bed load at the bottom of the river 

bed, while fine materials, sand and silt, are transported in suspension (Fruchart 2009).

A major property of sediments is their ability to adsorb small organic or inorganic compounds

(i.e. these compounds stick to the sediment particles); thus the transportation of organic or 

inorganic matter in the hydrosystem is largely facilitated by sediments. This means that 

sediments are actually a combination of mineral, inorganic and organic compounds with 

different properties. It also means that sediments largely facilitate the transportation of organic 

or inorganic matter in the hydrosystem. We summarize in Figure 2 the main components of 

sediments and detail these components below.

 2 Castro and Reckendorf (1995) detail further the components of the bedload: « Framework bedload refers to the 

larger particles that are moved only during large flow events. They create the structure of the bed. The matrix 

bedload refers to that part of the bed material that is small enough to be frequently entrained by low to moderate 

flows but is large enough to settle out of the water column in lower velocities. This also includes sediment 

deposited by intragravel flow. This would incorporate the sand and silt size material. The matrix bedload is often 

referred to as "sediment" by fisheries biologists and is the size class that is of most interest and concern in fisheries 

studies”.
8

Figure 2: Main components of river sediment

2.1 Sediment particle size

A standard classification of mineral sediments based on particle size is detailed in Table 1. 

Table 1: Conventional grain size ranges for different sediment types. Source: Ketelsen and Ward 2010
9

Welcomme (1985) gives a relationship between current speed and size of the sediment 

particles moved by the flow (Figure 3)

Figure 3: Relationship between flow speed and size of particles moved. Source: Welcomme 1985.

For the purpose of this report, we adopt a simplified classification reduced to three categories 

that are significant in the case of fish bioecology (Rowe et al. 2003):

• Coarse sediment, defined as particles larger than 0.95 or 1 mm. Being the main 

component of the river bed, affect the morphology of the river, shape fish habitats or 

spawning sites, and constitute the main biotope of several macro invertebrate species 

that fish feed upon;

• Sand or fine sediment, consisting of particles smaller than 0.85 mm which can be either 

bedded sediments or the suspended sediments depending on the river velocity 

(Figure 4).

• Silt and clay, i.e. particles smaller than 0.063 mm suspended in flowing water (thus 

creating its turbidity) or deposited into mud beds.
10

Figure 4: Nature of sediments depending on location, slope and current speed

In the case of the Mekong, a review of sediment-related information and data (Ketelsen and 

Ward 2010) led to the conclusion that “considerable skepticism surrounds Mekong sediment 

data, which has been collected with inconsistent methods, measuring different parameters and 

has often yielded widely divergent estimates”. 

Yet several authors agree that the dominant sediment categories in the Lower Mekong Basin 

are fine sands, silts and clays (Irvine et al. 2007, Sarkkula et al. 2009, Carling 2009). One of the 

few reliable sediment distribution curves available (cited in Ketelsen and Ward 2010, Figure 5) 

shows that in Pakse 99% of the sediment has a grain size smaller than fine gravel (>4.75 mm) 

and that 41% of the distribution is finer than coarse sand (>0.45 mm). In the Tonle Sap, silts and 

clays are the dominant grain size (Sarkkula et al. 2010). The latter authors conclude that the 

Mekong probably transports proportionally less sand and more silt/clay than other large rivers, 

and that clay and cohesive sediments seem to remain in suspension until the Mekong enters 

the Cambodian floodplain and the Mekong Delta.
11

Figure 5: Sample grain size distribution curve for Pakse (cited in Ketelsen and Ward 2010)

In this context, sand is, by contrast and considering its limited abundance, an important 

component for the ecology of the Mekong. Sand and sandy islands are a typical component of 

the wetland zone stretching between Pakse and Kratie (MRC BDP 2 zone 4, including the 

Siphandone wetlands) and an essential habitat for the biodiversity of the Mekong, as detailed 

for instance in Baird 2001, Bezuijen et al. 2008, Allen et al. 2008 or Meynell 2010. Sand 

transportation and dynamics (resuspension, movements of sand bars or in-channel 

consolidation) are directly dependent upon hydrodynamic conditions (Sarkkula et al. 2010), 

which implies that changes in these conditions may have a disproportionately large impact on 

the sandy habitats in the Mekong. More generally coarse materials are very important for the 

stability of the river bed as they constitute a carpet protecting the bottom of the river from 

incision by water-driven erosion; unfortunately coarse materials settle completely when 

entering dam reservoirs (see Figure 1), and cannot be flushed downstream (Fruchart 2009).

2.2 Sediments and organic matter

Sediment loads also include an organic component of great importance for the biological 

productivity of the river. This organic component is made of i) dissolved organic matter (e.g. 

degraded proteins from vegetal or animal origin, tannins) and ii) particulate organic material 

transported from the watershed slopes (pollen, leaves, branches, trees) and subject to 

biological degradation and size reduction (Welcomme 1985). Dissolved Organic Matter (DOM) 

is part of the water flow but is not sediment, whereas Particular Organic Matter (POM) is a part 

of the sediment load of rivers.

Importantly, a fraction of the organic matter is adsorbed onto sediment particles, which 

facilitates the transport of such matter but also influences their chemical dynamics: this 

adsorbed organic matter may be stored within deposited sediments, or may be reincorporated 

into the flow through erosion. (Welcomme 1985). 
12

In the case of the Mekong, the organic content amounts to 6-8% of the total sediment load 

(Pantulu 1986), which is seen as a large percentage and which contributes to the considerable 

productivity of the river. 

2.3 Sediments and inorganic matter 

River sediments serve as a major carrier and storage agent for inorganic nutrients such as 

phosphorus, nitrogen or potassium, but also pesticides and metals (Yang Xiaoqing 2003, Yi et al.

2008). As water contains low concentrations of dissolved nutrients, a river’s main nutrient load 

actually consists of nutrients associated with—or adsorbed on—sediments. Thus, 

measurements in North America and Europe showed that about 90% of the total phosphorus 

flux in rivers was associated with suspended sediment (Ongley 1996). The pattern seems to be 

similar in the Mekong (Meynell 2010).

The most important sediments for the transportation of nutrients are the very small size 

sediments such as clay and colloids. The sediments that are chemically active are those that 

are smaller than 63 mm (i.e. silt and clay), in particular for phosphorus, a nutrient highly 

attracted to ionic exchange sites that are associated with clay particles and with the coating 

common on these small particles (Ongley, 1996). In South America, rivers with high sediment 

loads and high alkalinity have higher concentrations of nitrogen and phosphorus—and thus are 

more productive—than rivers with clear water (Forsberg et al. 1988). Unlike phosphorus, the 

transport and fate of organic sediments or organic matter attached to sediments is complicated 

by microbial degradation. 

In the Mekong, the nutrients associated with sediments are responsible for the fertility of the 

floodplains and the delta (Meynell 2010). In particular, Sarkkula and Koponen (2010) showed 

that the high productivity of the Mekong floodplains is based on the nutrient loading associated 

with the sediments from upstream areas and that phosphorus is often the limiting nutrient. 

More specifically, 31-42% of the bioavailable phosphorus is transported into the floodplain with 

the sediment influx, which equates to 21,500 t/yr of bioavailable phosphorus (Sarkkula et al.

2010). Suspended inorganic material from the mainstream channel is often seen as more 

important to productivity than dissolved and particulate organic material (Vannote et al. 1980, 

Junk 1999).

The Mekong River Commission has defined quality classes for the main water parameters

(MRC 2007). These water quality classes are based on thresholds defined by French water-basin 

authorities and are detailed in 
13

Table 2: Parameters and thresholds used to classify the water quality in the Mekong. This table 

focuses on mineral and organic matter found in sediments. Source: MRC 2007

Class of water quality Very good Good Fair Bad Very bad

Organic matter and other matter that can be oxidized

DO (mg/l) ≥8 ≥6 ≥4 ≥3 <3

COD (mg/l O2) ≤5 ≤7 ≤10 ≤12 >12

NH4

-

(mg/l NH4) ≤0.5 ≤1.5 ≤2.8 ≤4 >4

Nitrogenous matter

NH4

-

(mg/l NH4) ≤0.1 ≤0.5 ≤2 ≤5 >5

Phosphorous matter 

TP (mg/l) ≤0.05 ≤0.2 ≤0.5 ≤1 >1

PO4

3-

(mg/l PO4) ≤0.1 ≤0.5 ≤1 ≤2 >2

Suspended matter 

TSS (mg/l) ≤5 ≤25 ≤35 ≤50 >50

2.4 Sediment loads

The amount of sediment transported by a river is another important factor in relation to fish 

biology and productivity. 

In the case of the Mekong there is limited knowledge and great uncertainty about the 

suspended sediment load and its variability. There is data—whose quality is disputed—on the 

suspended load, but there is no reliable data on bed load. This means that an ecologically 

important type of sediment transport that is affected by dams is not part of current analyses. 

(Kummu and Varis 2007, Ketelsen and Ward 2010).

It is now largely agreed that the total annual sediment discharge of the Mekong amounts to 

about 160 million tonnes per year (range 140 -180 Mt/y), which is high in comparison with 

other major rivers of the world (Meade 1996, Wolanski and Nguyen Huu Nhan 2005, Sarkkula 

et al. 2010, Ketelsen and Ward 2010). The total load of the Mekong is about the same as the 

Mississippi, 85% of that of the Yangtze River and 12% larger than that of the Amazon (Carling 

2009, Sarkkula et al. 2010,)3

. Under natural conditions, 50% to 60% of the sediments originate 

from China, the ‘Three S’ catchments contributing about 17 Mt/yr (i.e. about 10% of the total 

load) and the remainder of tributaries in the Lower Mekong Basin providing about 30% of the 

total load (Ketelsen and Ward 2010).

The Mekong’s sediment load is characterized by large intra-annual and inter-annual 

variability (Welcomme 1985, Ketelsen and Ward 2010 and Figure 6). On the seasonal level, 

water is heavily charged with silt during the rising flood, then deposits its suspended sediments 

 3 These figures are somehow disputed since Welcomme (1985) indicates 190 and 406 million tonnes of suspended 

load for the Mekong and Amazon respectively, but 560, 812 and 1625 million tonnes for the Yangtze, Brahmaputra 

and Ganges respectively. The Yangtze, Brahmaputra and Amazon are not part of Carling’s comparison.
14

over floodplains during the flood, and then becomes clear during the dry season (Welcomme 

1985). From an interannual-perspective, LMB tributaries contribute a greater proportion of the 

annual load during wet years, while in dry years the amount of input from China is higher than 

normal (Ketelsen and Ward 2010).

The Mekong’s sediment load is also characterized by strong geographical variability, the total 

suspended load increasing farther downstream. Thus, the annual total suspended load has 

been estimated as 67, 109 and 132 million tonnes per year at Chiang Saen, Vientiane and Khone 

Falls respectively (Carling 2009). Overall the Cambodian floodplains and Mekong Delta receive 

95% of the total suspended sediment flux from upstream (Kummu and Varis 2007) and 80% of 

the suspended sediments that enter the Tonle Sap Lake get deposited in its floodplain

(Lamberts 2006), which makes these intensive fishing grounds directly dependent on the flow 

conditions of the Upper Mekong (Baran et al. 2007a).

Figure 6: Annual average sediment load (1997-2004) at Kratie. Source: Kummu et al. in Ketelsen and 

Ward (2010) 
15

3 MEKONG FISH: CORE NOTIONS

The exceptional features of the Mekong fish resources have been detailed in several 

publications (e.g. Lagler 1976, Pantulu 1986, van Zalinge et al. 2003, Baran et al. 2007b, Hortle 

2009). We briefly review them here before focusing on the fish features related to sediments.

The Mekong is a place of exceptional fish biodiversity. The Mekong River is the world’s second 

richest river after the Amazon. The Tonle Sap is the lake with the highest fish biodiversity in the 

world after the East-African Great lakes. An analysis of lists of species and endangered species 

among 302 countries or territories worldwide shows that Lao PDR, Thailand and Viet Nam are 

among the top 5% for their number of freshwater fish species and number of threatened fish 

species. 

Fish biodiversity increases downstream and the 3S system is a hotspot. Like the sediment 

load, the Mekong River mainstream is characterized by a gradient of increasing species richness 

from the headwaters down to the sea, with 24 species in Tibet and 484 species in the Mekong 

Delta. A recent study (Baran et al. 2011) showed that within the Mekong Basin, the 3S system 

(Sekong, Sesan and Srepok watersheds) is home to 42% of the total Mekong fish biodiversity 

(i.e. 329 fish species out of 781), though the surface area of the 3S represents only 10% of the 

800,000 km2 of the Mekong watershed area. The 3S Rivers are also characterized by 17 

endemic species found nowhere else in the world.

The Mekong produces about 18% of the world’s freshwater fish yield. The fish catch, 

estimated to be between 755,000 and 2.6 million tonnes (the most reliable assessment being 

2.1 million tonnes), comprises about 18% of the global freshwater fish catch (range 6-22%), 

making the Mekong the largest inland fishery in the world. 

Mekong fish resources are essential to food security in the basin: Cambodia, Lao PDR and 

Thailand are the top four countries in the world for their freshwater fish consumption: fish 

consumption ranges between 24.5 and 34.5 kg/person/year. Thus, fish contributes 81% of the 

population’s protein intake in Cambodia and 48% in Laos. The economic value of Mekong 

capture fish is up to USD 2.2-3.9 billion per year. 

Fish migrations are an essential feature of the Mekong. Of the 189 migratory fish species 

known, 165 are long-distance migrants and these species represent more than 37% of the total 

yield, i.e. more than 770,000 tonnes per year. At the end of the dry season, more than 100 

migratory species (Ziv et al. 2012) migrate up tributaries to lay eggs in a riverine environment 

characterized by clear water and its associated seasonal flora and benthofauna.
16

Figure 7: Fish migration patterns in the Mekong. Source: Baran and Un, in press.

The exceptional abundance of Mekong fish resources is explained by a combination of high fish 

biodiversity, high productivity linked to high sediment load and flooding, and a high 

exploitation rate (Baran and Un, in press).

Figure 8: Factors explaining the size and importance of Mekong fisheries. Source: modified from Baran 

and Un (in press).
17

4 SEDIMENTS AND FISH BIOECOLOGY

Sediments constitute an important environmental factor in fish bioecology. Fish species 

inhabiting a river body are either adapted to specific sediment characteristics which are not 

constants (e.g. seasonal and inter annual variations) or tend to leave the area subject to 

excessive sediment load before returning after the event (flush flood, seasonal flood). Thus,

from a fish ecology viewpoint, the presence of sediments is normal; it is variation outside of the 

normal range that is detrimental to species, and there is no specific level at which all species of 

fish would be equally affected (Sanderson 2009).

Among rivers of the world there is a relationship between energy availability and sediment 

availability (Welcomme et al. 1989); in the Mekong the hydropower potential of the Lower 

Mekong Basin is estimated at 53,000 MW (ICEM 2010), with 30,000 for the Lower Mekong 

Basin alone (MRC 2001). The impact of such power extraction on the river nutrient availability 

deserves being studies in more detail.

Figure 9: relationship between energy availability and sediment availability. Source: Welcomme 1989

4.1 Sediments and fish respiration

Note: the issue of sediment overload and fish gill clogging is not detailed here since it is covered 

in the report “Reservoir sediment flushing and fish resources” also produced for the current 

project. 

There are two main sources of oxygen in the aquatic environment: the atmosphere and 

photosynthesis by plants. Oxygen from the atmosphere is diffused in the water through the 

air/water interface and this process is accelerated by wind and wave action; photosynthesis by 
18

aquatic plants, algae and phytoplankton is the most important source of dissolved oxygen in 

aquatic environment (Francis-Floyd 2011).

The organic component of sediments has a direct negative impact on dissolved oxygen 

through its Oxygen Demand. These organic compounds consume oxygen for oxidation 

processes, which reduces the amount of dissolved oxygen available in the water column 

(Welcomme 2001). WUP-FIN studies mentioned this phenomenon in the case of the Tonle Sap 

floodplain where sediment carried by the rainy season freshwater pulse can dramatically 

change dissolved oxygen levels and subsequently impact fisheries (Sarkkula and Koponen 2003, 

Koponen et al. 2005).

Suspended sediments also influence the amount of dissolved oxygen through their 

interference with photosynthesis. Two opposite pathways can be noted (UTAH State Water 

Plan 2010): i) turbidity reduces the amount of sunlight reaching the aquatic vegetation and 

thereby reduces its oxygen production (negative effect); ii) nutrients associated with suspended 

sediments favor plant growth and thereby increase their oxygen production (positive effect). 

Thus, dam development reducing sediment concentration would have opposite effects by 

simultaneously promoting and reducing plant-driven oxygen production (the release of hypoxic 

or anoxic reservoir water being ignored here). The combination of these different factors makes 

it difficult to predict the overall impact of sediment load reduction on oxygen concentration in 

water (Figure 10).

In the Mekong mainstream the average dissolved oxygen concentration in running waters 

ranges between 5.5 and 8.5 mg.l-1 (1985‐2005 data; MRC 2009). Dissolved oxygen 

concentrations below 5 mg.l-1 may be harmful to fish and piping (gulping air at the surface) is

observed when DO falls below 2 mg.l-1 (Francis-Floyd 2011). 
19

Figure 10: Influence of suspended sediment on oxygen content in water 

4.2 Sediments and fish nutrition

In the Mekong, there is not enough information to establish a detailed connection between 

sediment classes and the feeding of fish species. We reviewed for the present report the 

feeding of Mekong species in relation to sediments, as compiled in a literature review of 296 

Tonle Sap species (period covered: 1938-2003; Baran et al. 2007c) and detailed in FishBase 

(www.fishbase.org) and the Mekong Fish Database (MRC 2003). The information on diet 

contained in these two databases refers to the following food items and all their combinations: 

Detritus, Algae, Plants, Plankton, Zooplankton, Zoobenthos, Nekton, Animals and Insects. 

Although some of these categories (e.g. detritus, zoobenthos) reflect to some extent a 

sediment-related feeding mode, they are not explicit about the type of sediment involved.

Alternatively, Valbo-Jorgensen et al. (2009) review, from unspecified data, the food items of 

Mekong fish species, and find that mud feeders constitute 1% of Mekong fish species and that 

69 species are detritivores (Figure 11). 
20

Figure 11: Number and percentage of Mekong fish species feeding on various food sources. Source: 

Valbo-Jorgensen et al. 2009.

Evidence from other tropical rivers shows that sediment concentration influences i) the trophic 

food chains that fish are part of or depend upon, ii) the predator-prey relationship, and iii) the 

dominance of species in fish assemblages. We detail these aspects in the following paragraphs.

Fish nutrition and growth depends on the concentration and composition of sediments in the 

river. Fish sometimes feed directly on sediment (e.g. mullets), but more importantly sediments 

condition the presence and abundance of fish prey. The carbon component of sediments is the 

main food source of zooplankton and benthic invertebrates, and nutrients adsorbed on 

sediments are the main input for phytoplankton, algae and aquatic plant development. These 

first levels of the trophic pyramid constitute the diet of many fish species and are essential to 

fish productivity. Although the details of these very complex food webs are not well known, 

there is ample evidence that fish nutrition and productivity ultimately depends on the 

concentration and composition of sediments (in particular nutrients and organic particles)

available in the river (Gray and Ward 1982, Ward 1992, Power et al. 1996, Ongley 1996, USEPA 

2003).

Although the overall positive role of sediments on fish nutrition is clear, detailed processes 

are complex and sometimes in opposition: a decrease in sediment loads—and attached 

nutrients—might result in a reduction of primary production (UTAH State Water Plan 2010) but 

can also be favorable to primary production through increased irradiance (Lloyd et al. 1987). 

The latter phenomenon was observed on the Nile River, where a significant reduction in water 

turbidity (from 3000 to 15-40 mg-l

-1

) following sediment trapping by the Aswan dam resulted in 

increased phytoplankton density (Dubowski 1997); yet, the Nile fishery gradually collapsed 

(Bebars et al. 1996). In the coastal zone, maximal phytoplankton production is often found at 

some distance from the mouth of a river, in a zone of lower nutrient concentration, and this is 

related to increased light availability (Parsons 1977, Randall and Day 1987). Yet in the Mekong, 

Wyatt and Baird (2007) note a paradoxical effect: the sediment retention by the Yali Falls dam 
21

on the Sesan River resulted in increased sediment load and turbidity downstream due to 

increased riverbank erosion; this phenomenon in turn “reduced the light available for algal 

growth, or smothered bottom-growing algae, which are an important food source for some 

species”.

In the Mekong the link between upstream nutrients and fish abundance was already noted in 

1933 by Chevey: “A remarkable concentration of fish can be noticed at the mouth of the Bassac 

and Mekong Rivers at the beginning of the dry season. The fish are attracted by the enormous 

concentration of nitrogenous material coming from the Mekong” (Chevey 1933). In the South 

China Sea fish relying on Mekong river nutrients are found as far as 500 km from the river 

mouth (MRC 2003).

Overall, permanently reduced sediment loads modify food webs and result in a change in fish 

communities and dominant species. Following the closure of the Tucurui Dam (Brazil) and the 

downstream reduction in sediment load, the biomass of piscivorous fishes increased while that 

of planktivores diminished, and some species changed their diet (e.g. de Merona 2001). More 

generally Welcomme (2001), summarizing the impact of human interventions on fish, indicates 

that a decrease in suspended silt load results in changes in the fish community, with in 

particular a reduction in the number of non-visual predators and carnivores, and that a lack of 

sediment downstream of dams changes the nutrient cycle and causes a loss of illiophages (mud 

feeders). 

Permanently reduced sediment loads also alter the fish community structure and dominant 

species by altering fish predation patterns. Turbidity determines underwater visibility 

conditions, and it is now well established (review in Kerr 1995) that this in turn influences the 

predation efficiency of visually oriented fish species. Unlike species located at the bottom of the 

trophic pyramid, who usually filter water (planktivores) or forage at random (detritivores, 

bottom feeders), piscivorous predators mostly depend on their vision to catch prey. Turbidity 

subsequently influences the predator-prey relationship and ultimately the progressive 

dominance of specific predators and prey. Thus, de Melo et al. (2009) showed that in the 

Bananal floodplain (Mato Grosso, Brazil) changes to water transparency influence the 

composition of fish assemblages and dominant species among Cynodontidae. In estuaries 

Blaber et al. (1985) also report that predation, usually low due to high turbidity, can increase 

under specific conditions of clear and deep water. However, the relationship is not clear: 

reduced turbidity following retention of sediments by dams might favor top-level predators, 

but also the survival rate of prey that would better perceive predators. Overall, the literature 

review does not lead to clear conclusions about the impact of sediment retention on changes in 

trophic levels or the overall productivity of the fishery.
22

4.3 Sediments and reproduction

The main relationship between fish reproduction and sediment is through spawning grounds.

The reproductive guilds4 of fishes formalized by Balon (1975, 1981) and encompassing all the 

30,000 fish taxa are based on three main criteria: forms and functions in early development 

stages, features of reproductive behavior, and preferred spawning grounds. The latter makes 

extensive reference to the nature of the substratum where eggs are laid (Table 3).

Table 3: Main fish reproductive guilds. Guilds whose spawning is dependent on river sediment classes 

are highlighted in grey. Source: Balon 1981.

Ethological 

section

Ecological 

group Guild Meaning Notes

NONGUARDERS

Open 

substratum 

spawners

Pelagophils Pelagic spawners Numerous buoyant eggs

Lithopelagophils

Rock and gravel 

spawners with 

pelagic larvae

Embryos pelagic by positive 

buoyancy or active movement

Lithophils

Rock and gravel 

spawners with 

benthic larvae

Early hatched embryo hides 

under stones

Phytolithophils Nonobligatory 

plant spawners

Adhesive eggs on submerged 

items

Phytophils Obligatory plant 

spawners

Adhesive egg envelope sticks to 

submerged live or dead plants

Psammophils Sand spawners Adhesive eggs in running water 

on sand or roots over sand

Aerophils Terrestrial 

spawners

Small adhesive eggs scattered 

out of water

Brood hiders

Aeropsammophils Beach spawners Spawning above the waterline of 

high tides

Xerophils Annual fishes

Eggs and embryos capable of 

survival for many months in dry 

mud

Lithophils Rock and gravel 

spawners

Eggs buried in gravel depressions 

called redds or in rock interstices

Speleophils Cave spawners

Ostracophils Spawners in live 

invertebrates

GUARDERS Substrate 

choosers

Pelagophils Pelagic spawners Non-adhesive, positively buoyant 

eggs

Aerophils Above water 

spawners

Lithophils Rock spawners Strongly adhesive eggs, attached 

at one pole by fibers

Phytophils Plant spawners

 4 “A guild is defined as a group of species that exploit the same class of environmental resources in a similar way” 

(Root 1967)
23

Ethological 

section

Ecological 

group Guild Meaning Notes

Nest 

spawners

Aphrophils Froth nesters

Polyphils

Miscellaneous 

substrate and 

material nesters

Adhesive eggs attached singly or 

in clusters on any available 

substratum

Lithophils Rock and gravel 

nesters

Eggs always adhesive, free 

embryos

Ariadnophils Gluemaking nesters

Phytophils Plant material 

nesters

Psammophils Sand nesters

Thick adhesive chorion with sand 

grains gradually washed off or 

bouncing buoyant eggs

Speleophils Hole nesters

Actiniariophils Anemone nesters

BEARERS

External 

bearers 5 guilds

Internal 

bearers 4 guilds

This table illustrates the importance of sediments in river fish reproduction, and the very 

specific role of different sediment classes in fish spawning. 

For their reproduction some river fish species are dependent upon bedload while others are 

dependent upon washload. A number of fish species, in particular in upstream environments 

and in floodplains, spawn on the bottom and deposit their eggs in the empty spaces between 

gravel (e.g. croakers, lithophils) or on fine sediment and vegetation debris (e.g. some 

snakeheads). They may use their fins to create a microenvironment within the streambed with 

optimal water current and thus egg oxygenation (e.g. tilapias). Egg development requires a fine 

balance between discharge, velocity, and bed material for spawning to be successful. As 

opposed to this strategy, other species release their eggs in the water column (e.g. freshwater 

clupeids), and in this case egg development requires a fine balance between egg buoyancy and 

water/sediment density.

There is little information in the literature about the relationship between tropical fish 

reproduction and the impact of a reduced sediment load. If there is substantial information 

about sediments and fish in temperate rivers (in particular those with salmonids subject to 

sediment flushing), and about the spawning behaviors and preferences of East African lake fish 

species (in particular tilapias), overall the relationship between fish and sediments in tropical 

rivers is not well known, and reproduction as a physiological and behavioral process remains

largely understudied in environments characterized by a high number of species, a diversity of 

life strategies and few fish biologists. Thus, no substantial information has been generated at 

the crossing of two limited fields of research.
24

Furthermore, a considerable body of information details the impact of an increased sediment 

load (mainly due to erosion following deforestation, mining, etc.) on spawning, spawning sites, 

egg development and overall reproduction success in clear temperate streams (Kerr 1995, 

Castro and Reckendorf 19955), but very little information is available about the impact of a 

reduced sediment load on fish reproduction (i.e. the main focus of this report).

Freshwater fish at younger life stages are more vulnerable and more severely impacted by 

sediment variations than those at adult life stages (Alexander and Hansen 1986, Appleby and 

Scarratt 1989, Newcombe 1994). The most sensitive stage is the larval stage, more sensitive 

than the egg or juvenile stages (Appleby and Scarratt 1989, Isono et al. 1998). 

In estuaries, high turbidity is favorable to the larvae of many coastal fish species. These 

species tend to spawn in the coastal zone, and then larvae drift or actively migrate towards 

river estuaries where they find turbidity caused by a high concentration of suspended organic 

matter decreases the efficiency of predators and increases their survival rate (Blaber and Blaber 

1980, Cyrus and Blaber 1987a&b, Baran 1995, Lévêque and Paugy 1999).

A reduced sediment load tends to impact the reproduction success of species laying their 

eggs on river beds. In particular, when bedload transport is reduced, the riverbed’s sediments 

are not replaced by upstream sediments, which results in “armoring” of the riverbed. The 

resulting rockier riverbed is less suitable for the fish species that require specific substrate 

compositions for reproduction (Bizer 2000). Fish eggs directly exposed to water friction are also 

generally more vulnerable than eggs buried in the substrate (Newcombe 1994, Kerr 1995).

A reduced sediment load may impact the reproduction success of some species spawning in 

the water column (pelagophils). The eggs of these species must stay near the oxygenated 

water surface, which implies that their buoyancy matches the water density in the river at the 

time of spawning, the latter being driven by the water’s silt content. When oocytes are released 

and fertilized, they get hydrated, which increases egg volume several times and reduces their 

specific weight, prompting flotation and drifting (Carolsfeld et al. 2003). However, in the case of 

reduced silt content, eggs lose their buoyancy, sink and die. This phenomenon, relatively 

undocumented for river fish, is now well known for marine fish; e.g. Griffin et al. 2009, OspinaÁlvarez et al. 2012; it was flagged by Baran et al. (2007) as possibly having large-scale 

implications for the Tonle Sap fish resources. This buoyancy issue can also be significant in the 

case of juvenile fish (Pavlov et al. 1995, 2008)

 5 In their review, Castro and Reckendorf note that “Researchers have consistently found that the introduction of

excess matrix bedload can have disastrous results for the spawning habitat of fish that require gravel substrate for 

spawning.”
25

In the Mekong, the spawning grounds and the nature of these grounds have not been 

identified for the large majority of species (Chea Tharith et al. 2005). However, we reviewed 

for the present report the reproduction of Mekong species in relation to sediments, as 

compiled in a literature review of 296 Tonle Sap species (period covered: 1938-2003; Baran et 

al. 2007c) and detailed in FishBase (www.fishbase.org) and the Mekong Fish Database (MFD

2003). Findings are detailed below (Table 4)

Table 4: Tonle Sap species whose reproduction is or is not dependent on sediments.

Species whose reproduction is dependent on sediments

Probarbus 

jullieni 

Falling water and atmospheric 

temperatures, together with 

decreased turbidity, may be 

important factors in controlling the 

arrival time of Probarbus to its 

spawning grounds. The eggs are 

buoyant or semi-buoyant, but slightly 

heavy and adhesive. Generally 

intolerant of habitat alterations, it has 

disappeared from areas affected by 

impoundments. Large dams in Stung 

Treng and Kratie provinces would 

eliminate most of the rapids habitat 

that are important for the spawning 

of this species.

Baird and Flaherty 

2000; Ukkatawewat 

1999; Amatyakul et al.

1995; Rainboth 1996; 

Roberts 1992

Pangasius 

macronema 

It spawns in rapids in the beginning of 

the rainy season.

Schouten et al. 2000

Boesemania 

microlepis 

The identified spawning areas are 

characterized by being over 20 m 

deep, with hard rock or pebble and 

silt or sand substrate, and having slow 

to moderate counter-current eddies 

in the dry-season, and with steep rock 

sides descending into the pools.

Baird et al. 2001

Probarbus 

labeamajor 

Large dams on the mainstream in 

Stung Treng and Kratie provinces, 

would eliminate most of the rapids 

habitats that are important for its 

spawning.

Roberts 1992

Puntioplites 

proctozystron 

Spawning occurs in slow moving 

water areas with muddy bottom. The 

eggs are of the semi-buoyant type.

Watanadiroku and 

Murada 1985; Banyen 

et al. 1989a; Banyen 

et al. 1989b; 

Duangsawasdi et al.
26

1988; Banyen 1988

Channa 

gachua 

Spawns in shallow water with a silt or 

gravel substrate.

Talwar and Jhingran 

1992

Species whose dependence on sediments for reproduction is unclear 

Datnioides 

pulcher 

Spawns in March, the eggs are 

buoyant and approximately 0.8 mm in 

diameter.

Rithcharung and 

Mahawong 1993

Labeo 

chrysopheka

dion 

It is reported to spawn in swamps, 

flooded areas, or just upstream from 

shallow sandbars that line long river 

bends (Rainboth 1996). The eggs are 

semi-buoyant.

Smith 1945; Poulsen 

and Valbo-Jørgensen 

2000; Baird et al. 1999

Osteochilus 

melanopleur

us 

It is a pelagic spawner which produces 

semi-buoyant eggs.

Warren 2000; 

Watanadirokul et al.

1983; 

Osteochilus 

hasseltii 

Spawning occurs in floodplains in 

areas covered with submerged 

vegetation and gravel bottom. The 

eggs are buoyant or semi-buoyant.

Warren 2000; 

Pholprasith and 

Janesirisak 1972; 

Warren 2000; 

Pennapaporn et al.

1991

Pangasius 

conchophilus 

It seems likely that the species 

spawns at various times of year. An 

important spawning ground appears 

to be the Mekong mainstream 

somewhere between Kompong Cham 

and Khone Falls and in rapids and 

riffles of the Mun River.

Baird and Phylavanh 

1999; Poulsen and 

Valbo-Jørgensen 2000; 

Schouten et al. 2000
27

Chitala blanci Spawning takes place within the main 

river channel in areas with submerged 

wood and rocks, and the female 

guards the fry.

Poulsen and ValboJørgensen 2000

Chitala 

chitala 

Lays eggs usually on stakes or stumps

of wood, male fans them with tail, 

keeps them aerated and silt-free, 

guards them against small catfish and 

other predators.

MFD 2003

Species whose reproduction is not dependent on sediment

Clupeichthys 

aesarnensis 

It spawns pelagically probably in the 

upper water column close to the 

water surface although earlier 

reported to spawn at stumps, plant 

roots and grasses.

Scott and Crossman, 

1973; Soemarwotto 

and Costa-Pierce 1988

Corica 

laciniata 

It probably spawns at regular intervals 

throughout the year in the upper 

water column close to the water 

surface.

MFD 2003

Tenualosa 

thibaudeaui 

It spawns pelagically in open water. 

Developed eggs occur in March-June. 

In the Middle Mekong along the ThaiLao border, young of 40 to 50 mm 

total length were first encountered in 

the middle of April, but the 

abundance of juveniles increases 

during the onset of the rising water 

levels when the suspended solids 

increase.

Poulsen and ValboJørgensen 2000; 

Rainboth et al. 1975; 

Rainboth 1996

Amblyrhynchi

chthys 

truncatus 

Pelagic spawner, spawns in 

floodplains and mainstreams of large 

rivers during the wet season.

Warren 2000

Barbonymus 

altus 

It spawns pelagically in floodplains 

and flooded forests, or among 

flooded vegetation, and has buoyant 

or semi-buoyant eggs, with an initial 

diameter of 0.74 mm.

Warren 2000; Baird et 

al. 1999; 

Duangsawasdi et al.

1988
28

Cirrhinus 

microlepis 

It is a pelagic spawner and the eggs 

are buoyant or semi-buoyant.

Warren 2000; 

Pinyoying 1970

Cirrhinus 

molitorella 

It is a pelagic spawner, which 

produces buoyant or semi-buoyant 

eggs.

Warren, 2000

Cyprinus carp

io 

Open water/substratum egg 

scatterers with a fecundity of 281,936 

eggs/kg.

Skelton 1993

Labeo 

dyocheilus

This fish species spawns in AugustSeptember. It spawns pelagically in 

the mainstream in the wet season. 

Baird et al. 1999; 

Warren 2000

Puntioplites 

falcifer 

The spawning season is protracted 

with eggs reported in the period from 

March-December (with most reports 

from May-June), and 2 cm long 

juveniles reported all year (although 

in highest occurrence is from May to 

November). It is a pelagic spawner 

which lays buoyant or semi-buoyant 

eggs.

MFD 2003

Monopterus 

albus 

A bubble nest builder at the water 

surface near the shoreline during the 

rainy season.

Rainboth 1996; Talwar 

and Jhingran 1992
29

4.4 Sediments and migration

Changes in turbidity or water color are a migration trigger for at least nine of the Mekong 

migratory species. In the Mekong, 87% of the species whose migration status is known (i.e. 135 

species) are migratory species characterized by longitudinal or lateral migrations; out of these, 

more than 100 species are long-distance migrants (Ziv et al. 2012). Changes in turbidity or 

water color at the beginning of the rainy season are a migration trigger for at least nine of these 

species, which makes these species possibly sensitive to changes in sediment concentration.

These species are: Pangasius polyuranodon, Pangasianodon gigas and Pangasius bocourti 

(three catfishes, including a critically endangered species), Cyclocheilichthys enoplos and 

Paralaubuca typus (two cyprinids very dominant in catches), Bangana behri, Labeo 

chrysophekadion, Mekongina erythrospila and Tenualosa thibaudeaui (Baran 2006).

Fish migrations can play a significant role in nutrient distribution in a river basin. In South 

America, some “black water” hydrosystems are poor in nutrients (i.e. oligotrophic) with a 

limited in situ primary production, and yet they are characterized by a high fish biomass 

(Goulding et al. 1988, Polis et al. 1997). In fact, migratory fishes are the main vector of nutrient 

transfer from nutrient-rich turbid whitewater hydrosystems to nutrient-poor clear blackwater 

systems in South America (Kern and Darwich 1997, Winemiller and Jepsen 2004) and this 

system of "foodweb spatial subsidy" also characterizes mainstream-floodplain exchanges (Junk 

1999), temperate streams (Schuldt and Hershey 1995, Bilby et al. 1996) and estuaries (Deegan 

1993)

In the Mekong a similar process of nutrient transfer from nutrient-rich downstream 

floodplains towards more oligotrophic upstream tributaries via fish migrations is expected.

Thus at least 35% of the fish biomass is made of migratory species (Baran 2010) and the 3S 

system for instance is characterized by at least 89 migratory fish species representing 60% of 

the fishermen’s total catch (Baran et al. 2011); in the Tonle Sap River, more than 2000 tonnes 

of fish are harvested per day during the migration peak6

. If this process is confirmed, then a 

reduced sediment and nutrient load due to dam construction would result in a lower 

productivity of downstream floodplains, reduced fish migrations, and subsequently reduced 

nutrient transfer towards and productivity of the tributaries that are not directly subject to 

dams (Figure 12).

 6 Common catch rates during the days preceding the January full moon: 350 kg per haul, one haul every 15 mn for 

each “dai” net, 64 nets, 24 hours a day.
30

Figure 12: Reduction of nutrient transfers between river systems through reduced fish migrations.

4.5 Sediments and fish habitat

Fish habitat in tropical rivers should not be seen as a unique geographical area, but as groups of 

physically separated biotopes (feeding, spawning and nursery areas, dry season refuges) 

(Poulsen and Valbo-Jorgensen, 2001, Hortle 2009), plus the water quality inherent to these 

biota. Sediment plays a role in the characteristics of these habitats:

• geomorphology and bed substratum are determined by sediment loads;

• water turbidity is directly correlated with suspended sediment;

• pH of the water can be influenced by sediment.

Sediment load plays a major role in the geomorphology of river banks and river beds, two 

drivers of aquatic organisms’ communities, in particular fish. The composition of aquatic 

organism assemblages basically reflects i) the nutrient inputs and ii) the physical form of the 

river system (Welcomme 1985). The reduction of the upstream sediment load results in largescale changes in the downstream riverbed, the latter being a dynamic system in which 

sediments removed from the channel are replaced by the inflow of sediments from upstream.

This sediment reduction in turn makes river microhabitats less suitable for aquatic organisms 

that require specific substrate compositions for reproduction and/or foraging (Bizer 2000, 

Osmundson et al. 2002). Thus, the long-term ecological consequences of dams and other 

stream disturbances are related to such geomorphological changes (Trush et al. 1995, Pitlick 

and Van Steeter 1998).
31

A modification of the Mekong sediment concentration may affect deep pool fish habitats. In 

the Mekong, deep pools constitute a critical habitat for many fish species, especially during the 

dry season (Poulsen et al. 2002a, Baran et al. 2005, Viravong et al. 2006, Baird 2006).

Hydropower development on the Mekong would result in reduced flows in the rainy season 

and therefore less flushing of the sediments accumulated each year in the deep pools, i.e. 

increased sedimentation of deep pools (Conlan et al. 2008). However, dam construction would 

also reduce sediment concentrations and downstream bedload waves, resulting in a slower or 

reduced sedimentation process in pools. The balance of these two phenomena and the overall 

impact on deep pools as fish habitats is not well known.

Turbidity influences the distribution and abundance of fish in the main habitats of tropical 

rivers including river streams, floodplains, estuaries and river plumes. Several studies 

conducted in tropical floodplains have indicated that water transparency is a good predicator of 

fish assemblage composition and distribution (e.g. Tejerina-Garro et al., 1998; Pouilly and 

Rodríguez 2004). Turbidity is one of the parameters that strongly influences the distribution 

and abundance of communities in estuarine waters (Kennish 1990, Lévêque and Paugy 1999); 

thus Diouf (1996) based on a review of 50 studies in estuarine areas, shows that in 75% of the 

cases turbidity is one of the structuring factors of fish communities.

The community structure and abundance of fish species adapted to naturally turbid regimes 

can be affected by reduced sediment loads and flow regime regulation. Studies in South 

American floodplains showed seasonal changes in the relative abundance of visually and nonvisually oriented fish groups following water turbidity fluctuations (Tejerina-Garro et al. 1998).

In the Missouri River fish populations declined following the degradation of their habitats by 

river flow stabilization and sediment load reduction (Cross and Moss 1987, Pfleiger and Grace 

1987, Hesse et al. 1993).

Sediment concentration influences water pH. In most tropical rivers, the ionic composition of 

the water derives primarily from the rain and the rock or sediments over which river flows.

(Welcomme 1985). Fine sediment particles adsorb and neutralize dissolved humic acids (Ertel et 

al. 1986) and help maintain pH at values compatible with fish survival. Modifications in water 

pH can affect reproduction and other biological processes of fish. Extreme pH values, i.e. those 

below 4.5 or above 9.5, alter aquatic organisms’ ionic regulation and are usually lethal

(Gonzalez, 1996, Val et al. 1999)

In the Tonle Sap there are only 20 fish species whose ecological dependency on sediment is 

known. We reviewed for the present report the ecology of Mekong species in relation to 

sediments, as compiled in a literature review of 296 Tonle Sap species (period covered: 1938-

2003; Baran et al. 2007c) and detailed in FishBase (www.fishbase.org) and the Mekong Fish 

Database (MFD 2003). Findings are detailed below (Table 5).
32

Table 5: Tonle Sap species that are ecologically dependent on sediments.

Species whose ecology is dependent on sediments

Hypsibarbus 

lagleri 

May migrate into flooded forests

immediately adjacent to rivers, but 

does not occur over fine-grained 

sediments, preferring rocks instead.

Rainboth 1996

Homaloptera 

smithi 

Adults are found in high gradient 

streams over fast bedrock, cobble 

runs, and rapids, and juveniles occur 

in slower stretches of gravel and 

exposed tree roots.

Rainboth 1996; 

Krachangdara 1994; 

Rainboth 1996

Crossocheilus 

atrilimes 

Usually associated with clear, 

relatively fast waters with gravel or 

boulders.

Kottelat 2001

Opsarius 

koratensis 

Found over gravel substrate in clear, 

swift, small streams on rapidly 

flowing stretches of large rivers, 

especially areas with many rocks.

Rainboth, 1996; Baird 

et al. 1999

Tor sinensis Occurs in pools and runs over gravel 

and cobble in clear rivers in forest 

areas.

Rainboth 1996

Schistura 

pellegrini 

Inhabits shallow, clear, fast-flowing 

water over rocky bottoms in upland 

streams.

Rainboth 1996

Garra 

fasciacauda 

Inhabits rocky bottoms in fast 

flowing water of all sizes of rivers 

and streams.

MFD 2003

Garra 

cambodgiensis 

Inhabits rocky bottoms in swiftly 

moving water of small and mediumsized streams. 

MFD 2003
33

Setipinna 

melanochir 

Becomes abundant in the Middle 

Mekong when the water levels rise 

and turbidity increases. Inhabits 

shallow, clear, fast-flowing water 

over rocky bottoms in upland 

streams. 

Rainboth 1996

Macrognathus 

maculatus 

Found in lowland streams and peats. 

Often occurs in clear water over 

rocky bottoms in flowing streams.

Vidthayanon 2002

Mystacoleucus 

marginatus 

Found at bottom depths of rivers 

and streams. Inhabits areas with 

sand or gravel from small streams to 

large rivers.

Rainboth 1996

Hypsibarbus 

malcolmi 

Found in large rivers in the dry 

season and moves to medium-sized 

rivers in the wet season. Usually 

found over coarse substrate.

MFD 2003

Glossogobius 

aureus 

Found in rivers in clear to turbid 

water, usually over sand or gravel 

bottoms and mud.

Allen 1989; Allen et al.

2002

Mastacembelu

s favus 

Inhabits flowing waters. Most often 

found over gravel substrates where 

it buries itself during the day. 

MFD 2003

Tuberoschistur

a 

cambodgiensis

Inhabits sandy-bottomed streams. 

Previously found in a flowing stream 

with sandy bottom between Siem 

Reap and Kompong Thom near the 

Great Lake. Also found in sandy 

bottomed streams south of Phnom 

Penh.

Rainboth 1996
34

Hemibagrus 

nemurus 

This species occurs in most habitat 

types, but most frequently in large 

muddy rivers, with slow currents and 

soft bottoms.

Kottelat 1998

Channa striata Survives the dry season by 

burrowing into the bottom mud of 

lakes, canals and swamps as long as 

skin and breathing apparatus remain 

moist.

Davidson 1975

Pangio 

anguillaris

Found near the bottom over sand or 

silt substrate in debris and decaying 

vegetation. Spends much of its time 

buried in the sand or slowly foraging 

across the surface.

Rainboth 1996; 

Kottelat 1998

Macrognathus 

siamensis 

Spends much of its time buried in 

the silt, sand, or fine gravel with only 

a part of its head protruding from 

the bottom, but it emerges at dusk 

to forage for food.

Rainboth 1996

Macrognathus 

taeniagaster 

During the daytime, it spends much 

of its time buried in silt, sand, or fine 

gravel with only its snout and eyes 

protruding from the bottom, but it 

emerges at night to forage.

Rainboth 1996

Species whose dependence on sediments is unclear

Syncrossus 

helodes 

Found in small upland streams with 

fast currents, as well as at bottom 

depths of the Great Lake

Rainboth 1996

Cyprinus carp

io 

Feeds mainly by grubbing in 

sediments, whereby it often uproots 

aquatic plants and stirs up mud.

Scott and Crossman 

1973; Rainboth 1996
35

Lepidocephal

ichthys 

hasselti

Inhabits slow-moving, shallow 

waters of canals and inundated 

floodplains, usually on or in muddy 

substrates. Lives in swamps and 

rivers including peats. Also found in 

mountain streams, preferring sandy 

or gravelly bottom.

Rainboth 1996; 

Kottelat 2001; 

Vidthayanon 2002

Pseudobagari

us filifer

This species is present in the 

Mekong Basin, living in turbid, 

sandy-bottom lakes with moderate 

current.

Ng and Rainboth 2005

Nemacheilus 

pallidus 

This species is known to congregate 

in areas receiving direct sunlight 

such as shallow depths of small 

streams and rivers with sandy to 

muddy bottoms. It is found over 

sandy substrates with slow current. 

Rainboth 1996; 

Kottletat 2001

Polynemus 

aquilonaris

Found on sandy or muddy bottoms 

of freshwater rivers and estuaries. 

Motomura 2003

Species whose ecology is not dependent on sediment

Parachela 

oxygastroides

This species and P. siamensis seem to 

be more tolerant of high amounts of 

suspended solids than P. maculicauda

or P. williaminae and are more 

common in habitats disturbed by 

farming activities.

Rainboth 1996
36

5 SEDIMENTS AND FISH PRODUCTION

Nutrients transported by sediment loads are essential to fish productivity in tropical rivers.

Nutrients are essential to vegetation growth (phytoplankton, algae and plants), which 

constitutes the primary production level of aquatic food webs and determine the productivity 

of higher trophic levels. In tropical rivers, the majority of these nutrients are transported by the 

suspended sediment load. We detail in this section the linkages between sediments, flood 

pulses and fish production, and the consequences of reduced sediment load (oligotrophication) 

on river productivity.

The exceptionally high productivity of the river and its associated flood plains is explained by 

the river flood pulse. The flood pulse concept developed by Junk (Junk et al. 1989, Junk and 

Wantzen 2004) and based on the Amazon hydrosystem focuses on the lateral exchange of 

water, nutrients and organisms between a river or lake and the connected floodplains. This 

concept argues that the annual flood pulse is the most important aspect and the most 

biologically productive feature of a river ecosystem. The flood pulse is typically characterized by 

three main components: amplitude, duration and timing. Dam development results in reduced

sediment concentration downstream, but also in reduced amplitude of the flood and in a 

delayed flood (change in timing due to the filling of the dam reservoirs at the beginning of the 

rainy season). This combination of sediment retention and reduced hydrodynamic pulse may 

have a synergetic and negative effect on the overall productivity of the river downstream.

Figure 13: Flood pulse in the Tonle Sap Lake. Source: Osmose NGO, Cambodia.
37

The flood pulse concept is widely accepted as an explanation for the exceptional productivity 

of the Mekong floodplains and, in particular, the Tonle Sap, yet the Mekong system has some 

unique characteristics. Multiple authors have referred to the flood pulse as the driver of the 

productivity of the Mekong floodplains (e.g. Lamberts 2001 and 2006, Poulsen et al. 2002b, 

Sverdrup-Jensen 2002, Sarkkula et al. 2004, Davidson 2006, Baran et al. 2007a, Kummu et al.

2008, TKK and SEA-START RC 2009, Hortle 2009). Campbell et al. (2009) are the only authors

who reject this explanation, without providing many details. The relationship between the 

flood pulse and fish production has been underlined in particular for the Tonle Sap Lake 

(Sarkkula and Koponen 2003, Lamberts 2006, Halls et al. 2008, Lamberts and Koponen 2008, 

Kummu et al. 2008, Sarkkula and Koponen 2010). However, the Mekong system is distinct from

South American hydrosystems; in particular, the Mekong floodplains are covered with rice 

fields and are home to 11.3 million people, resulting in the release of local nutrients via artificial 

fertilizers, untreated sewage (60 million people, MRC 2003) and livestock (24 million heads, 

Nesbitt et al. 2004). However, it remains unclear whether these new sources of nutrients can 

compensate for those lost due to sedimentation behind dams. Furthermore, these expected 

additional nutrient inputs, in particular the phosphorus inputs, have to be analyzed in the 

context of the upcoming supply crisis expected at the global scale in the medium term (Roberts 

and Stewart 2002, Vaccari 2009, Cordell et al. 2009, http://phosphorusfutures.net)

If an abundant literature exists on eutrophication or naturally oligotrophic hydrosystems, 

very few studies have addressed dam-driven oligotrophication. Oligotrophication is the 

process by which a hydrosystem becomes nutrient-deficient and less productive, i.e. the 

opposite of the more common “eutrophication”. While eutrophication was considered in the 

last decades as one of the major environmental issues for hydrosystems under human 

influence, oligotrophication was perceived as an aesthetic improvement resulting in “clean” 

water, though from a fishery perspective, it also implies low productivity (Stockner et al. 2000).

Oligotrophication is mainly related to phosphorus deficiency, but the nitrogen/phosphorus 

ratio is also an important factor. Since phosphorus is much less soluble than nitrogen and 

leaches from the soil at a much slower rate, it is a more limiting nutrient of plankton and 

vegetation growth in aquatic systems than nitrogen. Consequently, oligotrophication most 

often results from a decrease in phosphorus, in particular in temperate systems. However, in 

some tropical aquatic systems nitrogen could also be the limiting factor (Moss, 1969, Guildford 

et al. 2003, Lehman and Branstrator 1993)

Oligotrophication results in changes to the food web structure (Stockner 1987, Tonn 1990,

Mann 1993 in Stockner et al. 2000). Nutrient-rich and productive hydrosystems (e.g. coastal 

upwellings, eutrophic lakes) are usually characterized by short food chains and productive fish 

resources (Cushing 1989, Ware and Thomson 1991). In hydrosystems that are becoming 

nutrient-poor, primary production declines and food chains become less energy efficient and 

become longer (Pomeroy 1974, Stockner and Porter 1988, Weisse and Stockner 1993).
38

Oligotrophication results in declining fisheries resources. Marked declines in yields from inland 

fisheries over the last 20–30 years in Europe and North America have largely been attributed to 

oligotrophication (Hartmann and Quoss 1993, de Bernardi et al. 1995, Ashley et al. 1997, Hess 

et al. 1982). Oligotrophication following dam construction also impacts fish production in the 

coastal zone (Marmulla 2001). Thus, in Cuba the reduction in sediment flow following the 

combination of river damming and reduced fertilizer use caused a dramatic decrease in the 

catches of estuarine species (Baisre and Arboleya 2006). In Brazil, a cascade of dams on the Sao 

Francisco river trapped 95% of the suspended sediment, reduced the nutrient concentration in 

the river plume by 90% and caused the estuary to become transparent, oligotrophic and 

unproductive (Knoppers et al. 2012). In Egypt, oligotrophication due to sediment trapping by 

the Aswan Dam has had a catastrophic effect on coastal fisheries at the mouth of the Nile River 

(El-Sayed and van Dijken 1995, Bebars et al. 1996)

In the Mekong the impact of oligotrophication on fish resources remains to be assessed. In 

particular, the role of phosphorus as a possibly constrained and limiting nutrient has not been 

established in the Mekong (Ongley 2009). Overall dam-driven oligotrophication is expected to 

significantly affect primary production and consequently the fish productivity of the Mekong; 

this correlation has been clearly established in the case of the Tonle Sap Lake (Sarkkula and 

Koponen 2010). However fish productivity decline is expected to be relatively more important 

in the Mekong Delta and in the sea area than in the Tonle Sap Lake (Sarkkula and Koponen 

2010). 

Overall, fish production in the Mekong is a multifactor phenomenon. It is clear that dam 

development will reduce the downstream sediment concentration, but will also minimize the 

flood pulse, alter water quality and block fish migrations. Fishery productivity resulting from 

these four drivers will be affected in multiple ways that cannot be related to sediments only

(Figure 14). Overall, our literature review confirms the major role—previously 

underappreciated—played by sediments and the need for new research to better assess the 

impact of oligotrophication on fisheries productivity. Ongoing hydrodynamic and physical 

modeling will clarify the retention rate of dams and the fate of sediments; however, what has 

not yet been addressed is the coupling between sediments and nutrients, and the amount of 

nutrients independent of sediment.

Figure 14: Relationship between dams, environmental or biological impacts and fish productivity.
39

6 CONCLUSIONS

In the Mekong, the total annual sediment discharge is about 160 million tonnes per year on 

average, with a wide range of intra-annual as well as inter-annual variability. Sediments in rivers 

are found in two main forms (suspended and bedded sediments) and they consist of a variety 

of particle sizes (roughly categorized as gravel, sand, clay and silt). Most of the sediment load in 

the Mekong is suspended. 

One property of sediments is that they adsorb and thus facilitate the transport of nutrients (in 

particular phosphorus and nitrogen) and organic particles. As dissolved nutrients in the water 

are generally low, the main nutrient load is associated with sediments. The dominant sediment 

categories in the Lower Mekong Basin are fine sands, silts and clays; the proportion of organic 

particles represents 6-8% of the total sediment load, which is considered high by global 

standards.

The Mekong is a place of exceptional fish biodiversity. Fish biodiversity increases downstream 

and the 3S system is a hotspot. The Mekong produces about 18% of the world’s freshwater fish 

yield. Mekong fish resources are essential to food security in the basin. Fish migrations are an 

essential feature of the Mekong. Sediments influence fishes’ biological functions, particularly

respiration, nutrition, reproduction and migration, but also their habitat. Nutrient load is also a 

dominant factor explaining the overall productivity of tropical river ecosystems (including 

floodplains, estuaries and coastal areas).

Respiration. The organic component of sediments has a direct negative impact on dissolved 

oxygen through its Oxygen Demand. Suspended sediments and adsorbed nutrients also 

influence the amount of dissolved oxygen in the water through their interference with plant 

photosynthesis. 

Nutrition. Sediments are the basic input for the food chains and trophic webs that fish are part 

of at a higher level, and thus are an essential component of fish nutrition. Suspended sediments 

and the turbidity they cause reduce photosynthesis and thus decrease primary production. 

Suspended sediments also play a role in predator-prey relationships. In the Mekong, a 

reduction of sediment loads is likely to result in decreased primary production, which might in 

turn change the dominant fish species and drive down fish productivity. But the relative 

influence of nutrients loads and turbidity on primary production must be clarified for this 

potential impact to be assessed. 

Reproduction. The main relationship between fish reproduction and sediments is through 

spawning grounds. In estuaries high turbidity is favorable to the larvae of many coastal fish 

species. There is little information in the literature about the relationship between tropical fish 

reproduction and the impact of a reduced sediment load.
40

Migrations. Changes in turbidity or water color are a migration trigger for at least nine of the 

migratory species in the Mekong. Fish migrations can play a significant role in the nutrient 

distribution in the river basin. In the Mekong fish constitute a nutrient transfer from nutrientrich downstream floodplains towards more oligotrophic upstream tributaries.

Habitat. Sediment load plays a major role in river geomorphology and in the riverbed and 

riverine habitats. Blocking sediment load will degrade the river bed downstream and will

therefore affect the aquatic organism communities adapted to these specific habitats. In the 

Mekong, deep pools, an essential habitat for the survival of numerous fish species during the

dry season, could be affected by modified water flows that result in an infilling of these pools, 

though this impact remains to be clarified. Water pH is also a characteristic of fish habitats that 

is related to suspended sediment concentrations.

The river flood pulse concept explains the exceptionally high productivity of rivers and their 

associated floodplains. It has been widely accepted as describing the exceptional productivity of 

the Mekong. Dam development is expected to reduce `the flood pulse as well as downstream 

sediment concentrations; this combination may have a synergetic and negative effect on the 

overall productivity of the river downstream, leading to its oligotrophication. This process of 

nutrient rarefaction, poorly studied, changes food web structures and decreases fisheries 

resources. Oligotrophication is most commonly related to phosphorus deficiency, but the 

nitrogen/phosphorus ratio is also to be considered. Ongoing hydrodynamic and physical 

modelling will also clarify the retention rate of dams and the fate of sediments, but the 

coupling between sediments and nutrients and the role of the amount of nutrients that are 

independent of sediments remain to be addressed.
41

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