You either need to turn up your warnings or actually listen to them:

Code:
beach.c:41:25: warning: format specifies type 'int' but the argument has type
      'double' [-Wformat]
  ...printf("%0d\n", mean_level);
             ~~~     ^~~~~~~~~~
             %0f
Also, you need to listen to the advice you've been given about indentation. Here's what your code *should* look like:

Code:
#include<stdio.h>
#include<math.h>

int main (void)
{
    int lake_ID, beach_number, number_of_samples, i;
    double number_of_organisms, mean_level=0, sum=0;

    FILE *in;

    in =fopen("july15", "r");

    while (fscanf (in, "%d" "%d" "%d", &lake_ID, &beach_number,&number_of_samples) != EOF)
    {
        {
            for (i=0; i<number_of_samples; i++)
                fscanf (in, "%lf", &number_of_organisms);
            sum = sum + number_of_organisms;
            mean_level = sum/number_of_samples;
        }

        if (number_of_samples < 3)
            printf ("%d Insufficient Data\n", beach_number );
        else if (mean_level > 50)
            printf ("%d closed\n", beach_number);
        else if (mean_level < 50)
            printf ("open\n");
        else if (beach_number<=0)
            printf("%0d\n", mean_level);

        if (lake_ID == 1 )
            printf ("Ontario:\n");
        else if (lake_ID == 2)
            printf ("Erie:\n");
        else if (lake_ID == 3)
            printf ("Huron:\n");
        else if (lake_ID == 4)
            printf ("Muskoka: \n");
        else if (lake_ID == 5)
            printf ("Simcone:\n");

        if (beach_number == 100)
            printf ("Kew Beach:\n");
        else if (beach_number ==101)
            printf ("Sunnyside Beach:\n");
        else if (beach_number ==103)
            printf ("Sandbanks:\n");
        else if (beach_number ==201)
            printf ("Port Dover:\n");
        else if (beach_number ==202)
            printf ("Port Burwell:\n");
        else if (beach_number ==203)
            printf ("Crystal Beach:\n");
        else if (beach_number ==301)
            printf ("Goderich:\n");
        else if (beach_number ==302)
            printf ("Sauble Beach:\n");
        else if (beach_number ==303)
            printf ("Kincardine:\n");
        else if (beach_number ==401)
            printf ("Muskoka beach:\n");
        else if (beach_number ==501)
            printf ("Sibbald Point:\n");
    }
    fclose(in);
    return(0);
}