Ideally, the industry will consist entirely or almost entirely of publically-listed companies. Extracting and aggregating information from their financial statements would then be straightforward. For private companies, promising sources of reliable financial information include industry trade associations, database vendors and specialist consultants.
For industries in the United States, the Stern school at New York University maintains a large database of margins and other financial data. http://pages.stern.nyu.edu/~adamodar/New_Home_Page/datafile/margin.html
You have received two valuable suggestions -- either to collect financial data from individual firms' financial reports (that can be presented on their websites, got from stock exchanges' mandatory company reporting or obtained from specialized vendors) or to look into already processed data of industry associations and especially state statistical bodies.
Be aware of two additional points:
1) in some cases it is easier to get information on the share of profitable firms in a particular industry than the absolute figures of profitability of sales (assets)
2) it is important how you define the industry you are researching. Sometimes SIC (Standard Industrial Classification) can be misleading. For example SIC Code 2037 (Frozen Fruits, Fruit Juices, and Vegetables) contains totally different technologies and largely different businesses.
First it may be better to conceptualize the variable of Profitability (to develop a working definition). There is another related variable called 'Profits'. I am not an accounting expert, but to my understanding, profitability is not profits but the organization's ability to earn profits within a particular period of future time. Hence, it can be considered as an subjective variable too (it is normally an objective variable, particularly profits). Then based on adequate and sound conceptualization and operationalization, it is possible to develop an instrument to measure the construct of Profitability. Then surveying can be done.
The concept of profitability needs to be qualified: as social (societal) or private (commercial) profitability. If we are looking for the commercial profitability we need to have detail costs of both direct and indirect of each flow of activities. The same is true with regard to the benefits. Then after having all these we can generate the variable of interest. For instance if the industry is constituted of firms each firm should have the direct costs directly related to their activities as well as the indirect costs, such as overhead costs coming from the industry level.
If we are interested to account some externalities (positive or negative) of the industry, then our profitability analysis have to account all these. Further more, in case of market distortion (especially in developing) in the price setting in the economy then price should be adjusted.
The majority of the above answers narrow their focus on financial outcome, a field I can offer little advice. However, I'd be interested in the reasons you ask the questions as the two further details are over what period & to whose benefit?
The latter question should look at concepts of Natural Capital in context of resource management & environmental sustainability. Many investment mechanisms look for design life of over 70 years, therefore the profitability over these longer timescales becomes significantly harder to calibrate.
For public and regulated companies, the national economic regulators could be useful and I would suggest the International Water Association (IWA) as a non-political resource to make introductions. Their online Publishing Digital Reference Library is an excellent resource although there are other specialised groups who could help you too.
Perhaps the easiest way is to first check if the National Statistics Office of this indicator does not calculate and publish? If this is not the case, you should collect data from economic entities in a given sector, sector and having information from individual companies and enterprises in this area, financial data, from financial statements it would be necessary to average this data to obtain average values for the entire sector. However, the problem may be the availability of data from all business entities, unless they are collected by specific offices as registers of basic financial data or a database of enterprises creating internet business cards of specific companies on the Internet. So the main issue is the availability of data from individual companies and enterprises. I invite you to the discussion