By using spectrophotometric method .

@chandan Ghosh: I already have chlorophyll-a values at discrete depths. And I want to calculate total chlorophyll-a concentration using chlorophyll-a values at different depths but trapezoidal integration provides value with units of mg/m2. How to get chlorophyll value in terms of mg/m3?

using  the published methods of chlorophyll determination , such as the method of Holden(1965), the results are given in mg per liter. It is very simple to convert these values as follows:mg per cubic meter =0.001mg per liter.

@Muayed Fadhil Abbas: Let me explain my doubt in another way: I have 3 chlorophyll a concentration values (in terms of mg/m3) at 3 discrete depths(for instance, 5m,25m,50m). I can calculate depth integrated chlorophyll a value over entire depth using trapezoid integration method but the resultant value will be in units of mg/m2 but i want to know if there any method to find depth averaged chlorophyll a value over depth of 50m in units of mg/m3?

One method that might meet your aim of study is by plotting depth value and chlorophyll value in a graph. For example, enter chlorophyll value in y axis and depth value in x axis. Application program that can be used is SPSS.  By using this plot, correlation between depth and chlorophyll can be estimated.  

@I Gede Ketut Adiputra: How do we know total or average chlorophyll-a value of defined depth of 0-50m from correlation plot? As the equation derived from plot will be able to give chla estimates at different depth.

OCM can give good result. Also acetone extraction followed by spectrophometric method is also good.

Apply square meter to cubic meter scale.  You will find the answer

x axis: 5, 25, 50 m

y axis: ...mg/m3,...mg/m3, ....mg/m3.

line drawn from these two axis would give estimation of chlorophyll a concentration per m depth in m3.  This is what I think that might go with your study.