I am not sure I understand your question. Maybe you can elaborate a bit. Do you mean why an assessment has to be done on ground and surface water at the same time to obtain a comprehensive understanding?
We have to go for conjunctive use of water for several reasons such as.
* rainfall is not distributed throughout the year so that the reservoirs are not filled always and not capable of delivering the required demands
* some reservoirs are not capable of delivering water for even single cropping cycle so that have to depend on other sources of water
* demand for water has increased not only from irrigated agriculture sector but also from other sectors such as industrial sectors, water supply. Therefore, to satisfy all the demands / needs, the management has to explore other sources
* environmental concerns have to be addressed (nowadays) when delivering water so that conjunctive use is essential
* in some instances, in order to keep the groundwater table below the root zone (drainage, salinity control etc.), conjunctive use of water has to be practiced
There could be many more reasons for the need to go for conjunctive use of water
Conjunctive use of water is not a wise solution to go for the supplying water into the dryland as it diverts and starves many of the native wetlands. In country like, India water crisis is common and dissent among the people still higher, hence it holds greats political and social implications. The best option is to go for re-vegetation using drip irrigation if the conditions are extremely dry and arid. Though this process is extremely slow but it ensures that groundwater get sufficiently recharged. Most of the parched and dry lands are so because of extensive ground water abstraction, high amount of grazing ruminants and denudation of vegetation. Population control measures and effective afforestation is probably only viable option keeping in long term sustainability of such projects.
Conjunctive use does need to be defined first. My understanding from an southeast australian perspective is that it's about using surface water and groundwater as one linked water source. The emphasis is more on the planning intent rather than on the hydrology/hydrogeology. That is, it recognises that it many areas extraction of one impacts on the other and so the only sensible approach is to manage them together. After a recent decade-long drought the effects of groundwater extraction on the sustainability of aquifers but also many surface water resources became a much more profound planning issue.
So my definition is a bit different to the first part of the definition in Wikipedia: http://en.wikipedia.org/wiki/Conjunctive_use. This is essentially using aquifers as a river water storage; filling them in wet years and extracting from them in dry times. I would argue this only one of many potential scenarios that could be described as conjunctive use. Even in that narrowly defined scenario whether it is a good thing depends on a whole range of things such as the sustainability of both surface water and groundwater, how connected they are, water quality, seasonal and demand patterns etc.
This FAO report is much more thorough than I can be on this matter:
http://www.fao.org/docrep/v5400e/v5400e0c.htm
This is not to say I disagree with the author above about groundwater extraction impacts on wetlands. I don't doubt it is occurring in the areas you describe Shivaji, and there is a profound effect on Australian wetlands in many areas because of loss of ground water availability. However, even in one location in Australia, groundwater extraction can impact or not on wetlands depending on the depth of the aquifer (deeper ones often disconnected) and the volumes being extracted.