本文将Base64编码形式的pdf文件加水印，并输出完成后的pdf的Base64编码，也可以根据情况自行改动，输出其他形式的内容。

首先引入两个包

        <!-- PDF文件依赖包 -->
        <dependency>
            <groupId>com.itextpdf</groupId>
            <artifactId>itextpdf</artifactId>
            <version>5.5.13.1</version>
        </dependency>
        <!-- PDF文件字体 防止中文乱码 -->
        <dependency>
            <groupId>com.itextpdf</groupId>
            <artifactId>itext-asian</artifactId>
            <version>5.2.0</version>
        </dependency>

 完整代码如下：

package com;

import com.itextpdf.text.Element;
import com.itextpdf.text.pdf.BaseFont;
import com.itextpdf.text.pdf.PdfContentByte;
import com.itextpdf.text.pdf.PdfGState;
import com.itextpdf.text.pdf.PdfReader;
import com.itextpdf.text.pdf.PdfStamper;
import sun.misc.BASE64Decoder;
import sun.misc.BASE64Encoder;

import java.io.BufferedOutputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileOutputStream;


public class testPdf {

    public static void main(String[] args) {

        try {

            String pdfBase64 = "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";
            String waterMarkName = "这是测试水印";


            BASE64Decoder base64Decoder = new BASE64Decoder();
            byte[] decodeBuffer = base64Decoder.decodeBuffer(pdfBase64);
            String outBase64 = PDFAddWatermark(pdfBase64, waterMarkName);
            // 为了验证结果方便，直接转为文件到本地
            FileOutputStream fos = new FileOutputStream("C:\\Users\\zh\\Desktop\\a.pdf");
            fos.write(base64Decoder.decodeBuffer(outBase64));
            fos.close();

        } catch (Exception e) {
            e.printStackTrace();
        }
    }


    /**
     * 给PDF添加水印
     * @param pdfBase64 原文件base64编码
     * @param waterMarkName 添加水印的内容
     */
    public static String PDFAddWatermark(String pdfBase64, String waterMarkName) throws Exception {
        // 每页水印行数
        int row = 7;
        // 每行水印个数
        int col = 3;
        // 旋转角度
        float rotation = 30f;
        BASE64Decoder base64Decoder = new BASE64Decoder();
        byte[] decodeBuffer = base64Decoder.decodeBuffer(pdfBase64);
        // 读取PDF
        PdfReader reader = new PdfReader(decodeBuffer);
        //创建字节数组输出流
        ByteArrayOutputStream ous =new ByteArrayOutputStream();
        // 创建字节缓冲输出流
        BufferedOutputStream bos = new BufferedOutputStream(ous);
        // 输出的PDF文件内容
        PdfStamper stamper = new PdfStamper(reader, bos);
        BaseFont base = BaseFont.createFont("STSong-Light", "UniGB-UCS2-H", BaseFont.EMBEDDED);
        PdfGState gs = new PdfGState();
        gs.setFillOpacity(0.2f);//改透明度
        gs.setStrokeOpacity(0.4f);//设置笔触字体不透明度

        PdfContentByte content;
        int total = reader.getNumberOfPages();//pdf文件页数
        for (int i=0; i<total; i++) {
            // 在内容上方加水印
            content = stamper.getOverContent(i+1);
            // 在内容下方加水印
            // content = stamper.getUnderContent(i+1);
            //开始写入
            content.beginText();
            content.setGState(gs);
            //字体大小
            content.setFontAndSize(base, 20);
            //每页7行，一行3个
            for (int j=0; j<col; j++) {
                for (int k=0; k<row; k++) {
                    float x = reader.getPageSize(i+1).getWidth() / col * j + 90;
                    float y = reader.getPageSize(i+1).getHeight() / row * k;
                    //showTextAligned 方法的参数（文字对齐方式，位置内容，输出水印X轴位置，Y轴位置，旋转角度）
                    content.showTextAligned(Element.ALIGN_CENTER, waterMarkName, x, y, rotation);
                }
            }
            // 添加水印文字
            content.endText();
        }
        stamper.close();
        //添加水印后pdf的base64
        byte[] bytes = ous.toByteArray();
        ous.close();
        bos.close();
        reader.close();
        return new BASE64Encoder().encode(bytes);
    }

}

结果展示a.pdf：