The core subject of this thesis is to assess the applicability of ocean colour algorithmsfor deriving chlorophyll and CDOM concentrations in east coast of Peninsular Malaysia waters. A series of bio-optical observations were conducted inthe study areaduring the2009seasons. These included in-water constituents (chlorophyll, suspended sediment and CDOM), absorption properties and reflectance. The analysis of the data reveals a clear seasonal signal with high valuesof all constituents and absorption properties during the northeast monsoon and low values during the southwest and inter-monsoon seasons. The timing, magnitude and spatial extent of these changesare associated withseasonal changes in hydrographic conditions (windforcing, sea surface temperature and freshwater input). Contrary to the trend during the monsoon seasons, inter-monsoon chlorophyll concentrations were higher offshore with some evidence of the pigment packaging effect.Inthe blue part of the spectrum, non-phytoplankton material (CDOM and detritus) is a dominant absorber (>70%of non-water absorption) regardless of the season andthis doesnot always covary with chlorophyll concentration.The performance of standard empirical and semi-analytical ocean colouralgorithms at retrieving chlorophyll concentration wasevaluated and validated using the bio-optical data in the study area. The results of our analysis showed that both typesof algorithmoften perform poorlyin the study area,either due to a wide range of variation in in-water constituentsor uncertainties in the spectral shape and magnitude of inherent optical properties.Using a series of in-situ bio-optical data, the algorithm best-suited for the study area was developed and evaluated. The results of this study indicate that a regionally-tuned chlorophyll algorithm can provide more accurate estimate of chlorophyll concentrationprovidedthat there exist a mean relationship between chlorophyll and CDOM, and the spectral shape of absorption does not change with varying environmental conditions. The most consistent resultof this study was that absorptions by phytoplankton and CDOMcan be well estimatedby a simple blue-green band ratio,offering a great opportunity to discriminatechlorophyll fromCDOM. Time-series of remote sensed distributions of chlorophyll, CDOM, sea surface temperature and wind speed were examined to evaluate variability of physical forcing and environmental conditions on seasonal and inter-annual variations in oceancolour in the study region. The results of this study confirm that thestrong seasonal and inter-annual cycles of chlorophyll and CDOM concentrationsarerelated to climatically driven cycles of monsoon and physical forcing (wind speed and SST). It is also shown that the annual cycle for both chlorophyll and CDOM concentrations is often overshadowed by inter-annual climate variability.