Not filled adhar number as well as caste certificate number in the time of filling the form

You say in the form you filled the above two are not mandatory. In such a case there should not be any problem. All mandatory columns should be filled. There should not be any mistake in the provided information. If you take care of these two things, I don't anticipate any issue.
If you are applying for any post under the reservation category based on the caste, you should attach a caste certificate and should mention the caste certificate number correctly. If you are not claiming for any reservation based on caste you need not mention the caste certificate number.
However, if they call you for certificate verification while attending that carry your caste certificate and Aadhaar card without fail. That may be helpful to you.

Yes, I come in reserved category, the caste certificate & aadhar card was mandatory and the number were not. As Im new in this field of government exams.. I don't have knowledge of the this.. And were I know for verification you must come with the certificates you have filled in the form at the time of registration. That's why I'm asking you , will that not giving numbers of my certificate will create any problem during my documents verification process

You have done a big mistake by not giving that information and it is likely that your application might be rejected later at the time of document verification. You are probably not very clear about the process of applying for any post after your education. When you apply you have to give all the information which can be used only in your favour and remember all the information should be checked for correctness before submitting. A single mistake would create a lot of inconvenience at a later stage. Please take the things seriously. It is a question of your career and whole life. Such opportunities do not come twice in your life.

Anyway, you have applied for some position in the water conservation department based on your diploma qualification. Now there is one thing that you can try and that is to send an email to them stating your mistake and apologise for it and then give the details of your Aadhaar number and SC certificate number and request them to consider these information along with the other information that you have already sent them earlier. Please remember to attach scanned copy of your these two documents with the email. I do not know whether postal and courier services are running or not otherwise in addition to the email it would be better to send these things to them by that also. Keep a copy of all this with you and when you go for document verification show it to them that you had already requested for that correction in your application and again most humbly requesting for that. The officials would definitely consider your case based on your request. Do not be perturbed and do this calmly and you would be considered for appearing in the examination or would be selected as per the procedure adopted by them.

While filling up your application in the water conservation department needing diploma engineers, you have filled up all the relevant details except the Adhar Card No and the Caste Certificate No. This might have happened due to your ignorance but this may be treated otherwise by the authorities treating the same as an act of concealment from your part.
Henceforth you must keep in your mind that entire details are to be filled up available in the form.
Now to rectify the error commited by you, you may send email stating the no of both the certificates as stated above with your due apology or still better send an application furnishing the details of both Adhar Card and your Cast Certificate and enclosures of photocopies of the same. This should be sent to the appropriate authority with the attachment of acknowledgement receipt along with your registered letter. Hope taking such a step from your end would save your candidature relating to the post.
During the stage of document verification, you may show the acknowledgment receipt along with details of Caste Certificate and Adhar Card.

You should be careful while applying for any jobs. As you said those details were not mandatory then this should not make any issues later. You can present those documents during the selection process, maybe at that time, you can enclose the documents. Caste certificate is essential if you fall any reservation category otherwise this will not create any issues.
For your satisfaction, you can visit the recruitment company's website and call them to get a better clarification on this. As per my understanding, if any field is not mandatory, will not create any issue during any phase of selection processes.
As you have mentioned in your comment, you have just missed entering the card/certificate number. So, no need to worry about it. Be relaxed and prepare well for other phases of selection processes.
Wish you all the very best.

As you stated that you had not filled details of Aadhar card and caste certificate in your application in the water conservation department. But as you had also mentioned that these details were not mandatory. So there must not be any problem.

As we know while filling inline application all the mandatory fields are marked by an asterisk sign (*) and without filling these mandatory fields we can not submit our application and even can not go to the next page of the application. Nowadays, Aadhar card details are asked to verify the details of the candidates and I think filling up of caste certificate number is not necessary.

During document verification, the department officials will check your all documents. And during that time you may be asked to submit one set of self-attested copies of all documents so no need to worry. No need to send any document to anyone. Just cool down and start preparing for your job.