Waleed,   Are you trying to count phytoplankton, zooplankton or both?  A haemocytometer is ok for single celled algae and smaller protozoa and rotifers.  Filamentous or colonial algae require different techniques.  Sometimes, depending on the question, you may want to quantitate algae using biomass or chlorophyll levels.  A Palmer Cell is also used for small algae and protozoa.  For larger algae and zooplankton, you would want to use something that works on a larger scale such as a Sedgewick-Rafter slide.  You can find these protocols in books such as Wetzel and Likens - Limnological Analyses or Lind - Handbook of Common Methods in Limnology.  If you would like a copy of the procedures for the different types of slides, you can email me, and I will send you a pdf of the protocols.  [email protected]

There is another problem when using hemocytometers for phytoplankton counts. Even if you have phytoplnkton in the right size range, you need fairly concentrated samples to get meaningful results. To get the samples concentrated you have to fix a 100 mL sample with lugols solution, let it settle on a slide under a co-called chimney, and then count under the microscope. You will need these chimneys, of course. Hope this helps a little.

Hemacytometers are great for counting dense samples of small algal cells (5-10 um) but a gridded Sedgewick Rafter is good for counting cells in the 15-50 um size range if the target cell is relatively dense. Whole water microplankton samples are easily counted when fixed w/ Lugol's solution and an aliquot is settled overnight in an Utermohl chamber. If you are wanting to count zooplankton; however, concentrate the sample to a known volume, mix well and remove an aliquot of sample using a stempel pipet. The aliquot can then be counted in a Ward counting chamber.

phyto or zoo plankton?

What is the range of cell diameter?

What microscope do you use?